OS: Microsoft Windows [Version 10.0.15063]
LibreOffice: Version: 5.3.6.1 (x64)
Build ID: 686f202eff87ef707079aeb7f485847613344eb7
CPU Threads: 4; OS Version: Windows 6.19; UI Render: default; Layout Engine: new; 
Locale: de-DE (de_DE); Calc: group
DirectX Version: DirectX 12
GFX Card: AMD Mobility Radeon HD 5000 Series
GFX Driver Name: aticfx64.dll,aticfx64.dll,aticfx64.dll,amdxc64.dll
GFX Driver File Version: 8.17.0010.1404 (English)
GFX Driver Version: 15.201.1151.1008
GFX DDI Version: 11.2
GFX Driver Model: WDDM 1.3
GFX Driver Date: 04.11.2015 02:00:00

The problem is as follows and didnt change over the last versions i used on the same machine described above:

A document, about approx. 110 pages long, containing lots of images holds a "protected against manual changes" Illustration Index (IL) at the top. The IL will be modified by hand, placing a "LS" and "LE" between a "#" on the entries structure, so it looks like "E"-"T"-"LS"-"#"-"LE". The manual modification is lost and reverted back to "E"-"T"-"#" whenever i perform one of the the following actions:

- close and reopen the document, or...
- update the IL manually, or...
- update all on document: Tools->Update->Update all, or...
- number of pages changes to more or lesser pages and right after that, one of the three previous steps listed is applied

There is no difference whether i use hardware acceleration or Open-GL for rendering the UI. The problem still persists, which is guess is a functional issue, rather than something related in the layout engine.

There is a similar bug filed here, but its filed for Linux: https://bugs.documentfoundation.org/show_bug.cgi?id=105624