The Bookmarks Manager should not remove or change anything unless you tell it to.

Are you using sync?

What is the link that was removed?

[v57+] Places Maintenance is built into Firefox.

Type about:support<enter> in the address bar.

You will find Places Database near the bottom. Press the Verify Integrity button.

similar to this thread - https://support.mozilla.org/en-US/questions/1216041

FredMcD #answer-1107197 Verify Integrity deleted bookmarks? https://bugzilla.mozilla.org/show_bug.cgi?id=1433423#c9

I think the Bugzilla guy means junk data is removed. Not old bookmarks.

FredMcD said What Junk?

Depending on how data is saved; When a file is changed, sometimes that process leaves behind non-data elements. Those elements are ignored, but they can build up over time.

By 'vacuuming' the data file, those non-elements are removed. (Simple explanation)

If you use Sync then best is to disconnect Sync temporarily during troubleshooting.

You can check for problems with the places.sqlite database (bookmarks and history) in the Firefox profile folder.

• use "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page

See also:

• http://kb.mozillazine.org/Locked_or_damaged_places.sqlite
• https://support.mozilla.org/en-US/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file

If "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page cannot repair places.sqlite then remove all places.sqlite files in the Firefox profile folder. Firefox will rebuild places.sqlite and restore the bookmarks from a recent JSON backup in the bookmarkbackups folder.

• keep a backup copy of places.sqlite in case a new places.sqlite database has to be created
• http://kb.mozillazine.org/Unable_to_process_the_backup_file_-_Firefox

You can use the button on the "Help -> Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page.

• Help -> Troubleshooting Information -> Profile Directory:
  Windows: Show Folder; Linux: Open Directory; Mac: Show in Finder
• http://kb.mozillazine.org/Profile_folder_-_Firefox