File > Recent Documents offers an item "Clear List". This functions unconditionally clears the complete list regardless an item is shown in the list (> PickListSize or ShowCurrentModuleOnly true) or flagged as favorite (see also bug 155698).
Yep we knew this would happen with implementation of bug 159120, see https://bugs.documentfoundation.org/show_bug.cgi?id=159120#c14 Kind of disconcerting that work on bug 155698, https://gerrit.libreoffice.org/c/core/+/157169 is not sufficient. More justification to get the full MRU history stanzas out of the user registry (registrysettings.xcu) and into a sub-folder/DB under the user profile. Then working with more robust pointers.