On pc Debian x86-64 with master sources updated today, I don't reproduce this.
But I must recognize I don't see any "icon 'Updates for Extensions available' appears on the right side of the menu bar".

However, I noticed this trace on console:
warn:legacy.osl:28866:28954:desktop/source/deployment/gui/dp_gui_updatedialog.cxx:549: OSL_ASSERT: false

Caolán: noticing https://cgit.freedesktop.org/libreoffice/core/commit/?id=4c3e0b2400c6b101a89f21e2268d5b696770fb9c, thought you might be interested in this one.

I think OSL_ASSERT should be a real assert here.
This line seems a bit weird:
m_xUpdates->set_id(nEntry, OUString::number(reinterpret_cast<sal_Int64>(pEntry)));

shouldn't we use pEntry->m_nIndex in a way?

Also, even if this line was before the quoted commit:
sal_uInt16 nIndex = sal::static_int_cast< sal_uInt16 >( m_enabledUpdates.size() );
can't we do more simple with:
sal_uInt16 nIndex(m_enabledUpdates.size());
?

Here's the small bt from this part:
#0  0x00007fff272a4d71 in dp_gui::UpdateDialog::insertItem(dp_gui::UpdateDialog::Index*, bool) (this=0x7fffe51ba5c0, pEntry=0x55555ba05410, bEnabledCheckBox=true)
    at /home/julien/lo/libreoffice/desktop/source/deployment/gui/dp_gui_updatedialog.cxx:549
#1  0x00007fff272a5043 in dp_gui::UpdateDialog::addEnabledUpdate(rtl::OUString const&, dp_gui::UpdateData const&) (this=0x7fffe51ba5c0, name="LanguageTool Version 4.6", data=...)
    at /home/julien/lo/libreoffice/desktop/source/deployment/gui/dp_gui_updatedialog.cxx:577
#2  0x00007fff272a354e in dp_gui::UpdateDialog::Thread::update(dp_gui::UpdateDialog::DisabledUpdate const&, dp_gui::UpdateData const&) const (this=0x55555c581cb0, du=..., data=...)
    at /home/julien/lo/libreoffice/desktop/source/deployment/gui/dp_gui_updatedialog.cxx:437
#3  0x00007fff272a2804 in dp_gui::UpdateDialog::Thread::execute() (this=0x55555c581cb0) at /home/julien/lo/libreoffice/desktop/source/deployment/gui/dp_gui_updatedialog.cxx:324
#4  0x00007ffff64a058e in salhelper::Thread::run() (this=0x55555c581cb0) at /home/julien/lo/libreoffice/salhelper/source/thread.cxx:40

yeah, the return value there is wrong. Though luckily the return is unused so we can just remove that https://gerrit.libreoffice.org/#/c/79270/

Moving to ASSIGNED

A few problems. The above patch is just cosmetic as the bad return value isn't used.

Normally this update dialog is a sub dialog of the extension manager. In this case it is a toplevel, but still creates the extension manager window, but doesn't execute it. So its there but not running. The assumption was that if the window existed it was executing. https://gerrit.libreoffice.org/#/c/79281/ fixes that assumption. Which is the crash problem I believe.

https://gerrit.libreoffice.org/#/c/79282/ fixes the locked ui, where there is one more lock than unlock around the update dialog. The presence of the tooltip-alike window is the problem there, treating FloatingWindows like Tooltips solves that for me.

These cases where there is a modeless dialog (extension manager, whether visible or not) which has modal child dialogs which want to be modal to the entire application are a pain.

Caolán McNamara committed a patch related to this issue.
It has been pushed to "master":

https://git.libreoffice.org/core/commit/9b231713790c6e94eb64c3fc108ce99ebd2b90af

Related: tdf#127645 return value is unused

It will be available in 6.4.0.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

Caolán McNamara committed a patch related to this issue.
It has been pushed to "master":

https://git.libreoffice.org/core/commit/243db6880cf1337de237e258fad1524413db848c

Resolves: tdf#127645 ignore floating windows like we do tooltips

It will be available in 6.4.0.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

Caolán McNamara committed a patch related to this issue.
It has been pushed to "master":

https://git.libreoffice.org/core/commit/5110beb7f0821b7c63f9947a6df7256da559b6c9

Related: tdf#127645 update dialog has a slave extension dialog

It will be available in 6.4.0.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

Looks right for me in master now, backports to 6-3 in gerrit

Checked with: 

Version: 6.4.0.0.alpha0+ (x64)
Build ID: b2d8093b19642038631dfb8f1ab6745a380a652c
CPU threads: 4; OS: Windows 10.0; UI render: default; VCL: win; 
TinderBox: Win-x86_64@42, Branch:master, Time: 2019-09-23_22:42:37
Locale: de-DE (de_DE); UI-Language: en-US
Calc: threaded

LibreOffice still crashes if you perform the steps 1 to 5 of original description. At step 9 LibreOffice does not freeze any longer. 

LibreOffice also still crashes if you perform these steps:

[1] Start LibreOffice.
[2] Install an extension, that is not current.
[3] Close Extension dialogue and restart LibreOffice.
[4] Wait until the icon 'Updates for Extensions available' appears on the right side of the menu bar.
[5] Open Extension Manager and click Check for Updates. The dialogue “Extension Update” is displayed: A more up to date version of the extension is available.
[6] Close dialogues 'Extension Update' and 'Extension Manager'.
[7] Click the icon 'Updates for Extensions available' in the menu bar. LibreOffice crashes. Expected: No crash.

Set status back to UNCONFIRMED, because the bug has not been confirmed yet.

Harald: would it be possible you attach a backtrace? (see https://wiki.documentfoundation.org/QA/BugReport/Debug_Information#Windows:_How_to_get_a_backtrace)

(In reply to Julien Nabet from comment #11)
> Harald: would it be possible you attach a backtrace? (see
> https://wiki.documentfoundation.org/QA/BugReport/Debug_Information#Windows:
> _How_to_get_a_backtrace)

Yes, I will try to do this but it may take some time, because I have not done this yet.

Meanwhile I produced a crash report with version 6.3.1.2:

crashreport.libreoffice.org/stats/crash_details/f81445af-6a20-4e4d-8ffb-a3a05c558f5b

This report was created at step 6 of the original report. With version 6.4.0.0.alpha0+ there was no request for sending a crash report.

Created attachment 154459 [details]
Backtrace of crash

Thank you Harald for your feedback.
I must recognize I've got no clue here about the culprit.

(In reply to Harald Koester from comment #13)
> Created attachment 154459 [details]
> Backtrace of crash

Hi Caolán,
Does the backtrace ring a bell for you ?

Caolán McNamara committed a patch related to this issue.
It has been pushed to "libreoffice-6-3":

https://git.libreoffice.org/core/commit/00aaada667af4d7138e3ddca153c37afd5f61f23

Resolves: tdf#127645 ignore floating windows like we do tooltips

It will be available in 6.3.3.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

Caolán McNamara committed a patch related to this issue.
It has been pushed to "libreoffice-6-3":

https://git.libreoffice.org/core/commit/cb5be6961e071ea2b9efd66cd62b98ffda5a058f

Related: tdf#127645 update dialog has a slave extension dialog

It will be available in 6.3.3.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

I can reproduce this under gen

in

Versión: 6.3.3.1 (x86)
Id. de compilación: f41f4c7f9507aeca13cb9df51f34d80e8ba30a99
Subprocs. CPU: 1; SO: Windows 6.1; Repres. IU: predet.; VCL: win; 
Configuración regional: es-ES (es_ES); Idioma de IU: es-ES
Calc: threaded

I get this crash: http://crashreport.libreoffice.org/stats/signature/com::sun::star::configuration::theDefaultProvider::get(com::sun::star::uno::Reference%3Ccom::sun::star::uno::XComponentContext%3E%20const%20&)

if I do:
1. Install LanguageTool 4.2.
2. Right after installing it -> Check for updates
3. Close the check for updated dialog

-> Crash

Caolán McNamara committed a patch related to this issue.
It has been pushed to "master":

https://git.libreoffice.org/core/commit/3ca92aee38c98ba6e0a21d8531321ca2f0ab6968

Resolves: tdf#127645 fix crash on revisit to check updates

It will be available in 6.4.0.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

Caolán McNamara committed a patch related to this issue.
It has been pushed to "libreoffice-6-3":

https://git.libreoffice.org/core/commit/3adeac61eee9f681b9791936e06cdb016574fc6e

Resolves: tdf#127645 fix crash on revisit to check updates

It will be available in 6.3.4.

The patch should be included in the daily builds available at
https://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
https://wiki.documentfoundation.org/Testing_Daily_Builds

Affected users are encouraged to test the fix and report feedback.

*** Bug 128592 has been marked as a duplicate of this bug. ***

Let close this issue as RESOLVED FIXED