Her's an entry I made to delete the recent file list in the ebook reader/converter Stanza Desktop.
[stanza Desktop*]
LangSecRef=3021
Detect=HKCU\Software\JavaSoft\Prefs\stanza\container\swt
Default=False
RegKey1=HKCU\Software\JavaSoft\Prefs\stanza\container\swt\recent
You could replace 'recent' with 'bookmarks' or 'positions' to delete all bookmarks or the last positions of opened files.