Funky footnote issues, including a missing footnote #

My environment is LibreOffice on Windows 7 SP1

In a particular monograph, I experience the following footnote anomalies.

Typically, I can delete footnotes by selecting the footnote number (“anchor”) in the main text and hitting the Delete key (just as you would expect). Footnote #1, when I attempt this, is NOT deleted; it remains at the bottom of the page even though its associated anchor (in-text reference) is gone. While I can proceed to delete the text of this footnote, I cannot get rid of the note’s number. This item remains in the footnote chain (i.e., I can navigate through the footnotes page by page, and this first footnote is part of that chain).

Footnote #4 does not exist. If I insert a note ahead of #5, the new note becomes #5 and the following notes are renumbered. Footnote 4 seems to be impossible to create.

This monograph contains a “section” (labeled “Analysis”). When I open the dialog Format > Sections… > Options > Footnotes/Endnotes, I might, for example, check “Collect at end of text” and set “Restart numbering” to 1. Nothing happens. Nothing ever happens / changes no matter what I try to apply using this dialog.

Is there anything I can do to make these things work? I particularly would like to eliminate the gap in the footnote numbers.

If this strange behavior only happens in a single file, it’s possible that it has become somewhat corrupted - not bad enough to become unreadable, but still corrupted. That can sometimes be fixed by wholesale copy/paste to a new, blank document.
If it happens more often, it may help to reset your user profile. See Frequently asked questions - General - The Document Foundation Wiki - important: rename the folder, don’t delete it.

Copy & paste did make footnote #1 deletable but did not solve the problem of not being able to insert footnote #4 or renumber the footnotes. [And copying doesn’t handle my complicated headers and footers, sadly.] Good suggestion and may help me out sometime. Thanks.

This behavior is happening to me in v., and I reset my profile barely a week ago after a different odd behavior. I’ve deleted two footnotes in the text, and the footnotes disappear but navigation still goes to the place in the text where they were. I deleted a large section of surrounding text; there is still a phantom footnote, and the first real footnote has the number 2.