Updater issue after update to 16.3.1

Hello,
We have recently updated our XWiki from 14.7 to 16.3.1
We had fighting with extensions, still do, but Extension Updater does not work.
We receive a page with error


and having the following log entries in catalina.out:

2024-06-25 16:21:38,200 [ajp-nio-127.0.0.1-8009-exec-10 - https://10.132.168.147:8443/xwiki/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=XWiki.ExtensionUpdater] WARN  i.t.XWikiTransformationManager - Failed to locate transformation with hint [numberedheadings], ignoring it. Root reason [ComponentLookupException: Can't find descriptor for the component with type [interface org.xwiki.rendering.transformation.Transformation] and hint [numberedheadings]]
2024-06-25 16:21:38,200 [ajp-nio-127.0.0.1-8009-exec-10 - https://10.132.168.147:8443/xwiki/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=XWiki.ExtensionUpdater] WARN  i.t.XWikiTransformationManager - Failed to locate transformation with hint [numberedfigures], ignoring it. Root reason [ComponentLookupException: Can't find descriptor for the component with type [interface org.xwiki.rendering.transformation.Transformation] and hint [numberedfigures]]
2024-06-25 16:21:38,205 [ajp-nio-127.0.0.1-8009-exec-10 - https://10.132.168.147:8443/xwiki/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=XWiki.ExtensionUpdater] ERROR o.a.v.parser                   - xwiki:XWiki.XWikiPreferences: Encountered "<EOF>" at line 18, column 10.
Was expecting one of:
    "\u001c" ...
    "\u001c" ...
    "||" ...
    "|" ...
    "(" ...
    ")" ...
    <ESCAPE_DIRECTIVE> ...
    "]]#" ...
    <WHITESPACE> ...
    <NEWLINE> ...
    <SUFFIX> ...
    <STRING_LITERAL> ...
    <INTEGER_LITERAL> ...
    <FLOATING_POINT_LITERAL> ...
    <DOT> ...
    "{" ...
    "}" ...
    "\\\\" ...
    "\\" ...
    <TEXT> ...
    <INLINE_TEXT> ...
    <EMPTY_INDEX> ...
    "{" ...
    "\u001c" ...

Can you help us to repair this page?

These 2 are just warnings and they mean that you’ve setup some transformations in xwiki.properties for which the extensions are not installed.

I think this one could be caused by a bad merge during the upgrade of the XWiki.XWikiPreferences page. You could check the history of that page by using http://localhost:8080/xwiki/bin/view/XWiki/XWikiPreferences?viewer=history (replace the server part by your domain) and then doing some diffs to see what has been changed.