Are you using Sync to sync the bookmarks ?

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

This could be a problem with the places.sqlite and favicons.sqlite files in the Firefox profile folder.

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

If errors are reported with "Verify Integrity", close and restart Firefox or reboot and retry.

If "Verify Integrity" cannot repair places.sqlite, rename/remove all places.sqlite and favicons.sqlite files in the Firefox profile folder with Firefox closed. Firefox will rebuild places.sqlite and restore the bookmarks from the most 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
• you lose the history when a new places.sqlite is created

You may have to restore an older bookmarks backup in the bookmarkbackups folder via the Bookmarks Manager (Library).

• Bookmarks -> Show All Bookmarks -> Import & Backup -> Restore
• https://support.mozilla.org/en-US/kb/restore-bookmarks-from-backup-or-move-them

See also:

• https://support.mozilla.org/en-US/kb/fix-bookmarks-and-history-will-not-be-functional
• https://support.mozilla.org/en-US/kb/cant-add-change-or-save-bookmarks

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

• Help -> More Troubleshooting Information -> Profile Folder/Directory:
  Windows: Open Folder; Linux: Open Directory; Mac: Show in Finder
• https://support.mozilla.org/en-US/kb/profiles-where-firefox-stores-user-data

This in the integrity panel.

> Task: checkIntegrity + The places.sqlite database is sane + The favicons.sqlite database is sane > Task: invalidateCaches + The caches have been invalidated > Task: checkCoherence + The database is coherent > Task: expire - The task queue was cleared by an error in another task. > Task: originFrecencyStats - The task queue was cleared by an error in another task. > Task: vacuum - The task queue was cleared by an error in another task. > Task: stats - The task queue was cleared by an error in another task. > Task: _refreshUI - The task queue was cleared by an error in another task.

The presence of lines like "The task queue was cleared by an error in another task" is a clear indication that something is wrong with your places.sqlite database and you need to follow the steps I posted above starting with closing and restarting Firefox (you may have to restart more than once).

integrity . the full list

> Task: checkIntegrity + The places.sqlite database is sane + The favicons.sqlite database is sane > Task: invalidateCaches + The caches have been invalidated > Task: checkCoherence + The database is coherent > Task: expire + Database cleaned up > Task: originFrecencyStats + Recalculated origin frecency stats > Task: vacuum + Initial database size is 10240KiB + The database has been vacuumed + Final database size is 5120KiB > Task: stats + Places.sqlite size is 5120KiB + Favicons.sqlite size is 13824KiB + pragma_user_version is 68 + pragma_page_size is 32768 + pragma_cache_size is -2048 + pragma_journal_mode is wal + pragma_synchronous is 1 + History can store a maximum of 71300 unique pages + Table moz_origins has 555 records + Table moz_places has 3660 records + Table moz_historyvisits has 5935 records + Table moz_inputhistory has 0 records + Table moz_bookmarks has 43 records + Table moz_bookmarks_deleted has 0 records + Table moz_keywords has 0 records + Table sqlite_sequence has 1 records + Table moz_anno_attributes has 3 records + Table moz_annos has 48 records + Table moz_items_annos has 0 records + Table moz_meta has 7 records + Table moz_places_metadata has 0 records + Table moz_places_metadata_search_queries has 0 records + Table moz_places_metadata_snapshots has 0 records + Table moz_places_metadata_snapshots_extra has 0 records + Table moz_places_metadata_snapshots_groups has 0 records + Table moz_places_metadata_groups_to_snapshots has 0 records + Table moz_session_metadata has 0 records + Table moz_session_to_places has 0 records + Table moz_previews_tombstones has 0 records + Table sqlite_stat1 has 18 records + Pages sequentiality: 71.8 + sqlite_schema: 32KiB (0.8%), 30.2% eff. + moz_origins: 32KiB (0.8%), 64.2% eff. + sqlite_autoindex_moz_origins_1: 32KiB (0.8%), 60.1% eff. + moz_inputhistory: 32KiB (0.8%), 0% eff. + sqlite_autoindex_moz_inputhistory_1: 32KiB (0.8%), 0% eff. + moz_bookmarks: 32KiB (0.8%), 9.1% eff. + moz_bookmarks_deleted: 32KiB (0.8%), 0% eff. + sqlite_autoindex_moz_bookmarks_deleted_1: 32KiB (0.8%), 0% eff. + moz_keywords: 32KiB (0.8%), 0% eff. + sqlite_autoindex_moz_keywords_1: 32KiB (0.8%), 0% eff. + sqlite_sequence: 32KiB (0.8%), 0.1% eff. + moz_anno_attributes: 32KiB (0.8%), 0.3% eff. + sqlite_autoindex_moz_anno_attributes_1: 32KiB (0.8%), 0.3% eff. + moz_annos: 32KiB (0.8%), 9.4% eff. + moz_items_annos: 32KiB (0.8%), 0% eff. + moz_meta: 32KiB (0.8%), 1.3% eff. + moz_places_metadata: 32KiB (0.8%), 0% eff. + moz_places_metadata_search_queries: 32KiB (0.8%), 0% eff. + sqlite_autoindex_moz_places_metadata_search_queries_1: 32KiB (0.8%), 0% eff. + moz_places_metadata_snapshots: 32KiB (0.8%), 0% eff. + moz_places_metadata_snapshots_extra: 32KiB (0.8%), 0% eff. + moz_places_metadata_snapshots_groups: 32KiB (0.8%), 0% eff. + moz_places_metadata_groups_to_snapshots: 32KiB (0.8%), 0% eff. + moz_session_metadata: 32KiB (0.8%), 0% eff. + sqlite_autoindex_moz_session_metadata_1: 32KiB (0.8%), 0% eff. + moz_session_to_places: 32KiB (0.8%), 0% eff. + moz_previews_tombstones: 32KiB (0.8%), 0% eff. + sqlite_stat1: 32KiB (0.8%), 3% eff. + moz_places_visitcount: 32KiB (0.8%), 90.4% eff. + moz_bookmarks_itemindex: 32KiB (0.8%), 1.4% eff. + moz_bookmarks_parentindex: 32KiB (0.8%), 1.4% eff. + moz_bookmarks_itemlastmodifiedindex: 32KiB (0.8%), 2.4% eff. + moz_bookmarks_dateaddedindex: 32KiB (0.8%), 2.1% eff. + moz_bookmarks_guid_uniqueindex: 32KiB (0.8%), 2.6% eff. + moz_keywords_placepostdata_uniqueindex: 32KiB (0.8%), 0% eff. + moz_annos_placeattributeindex: 32KiB (0.8%), 1.7% eff. + moz_items_annos_itemattributeindex: 32KiB (0.8%), 0% eff. + moz_places_metadata_placecreated_uniqueindex: 32KiB (0.8%), 0% eff. + moz_places_metadata_referrerindex: 32KiB (0.8%), 0% eff. + moz_places_metadata_snapshots_pinnedindex: 32KiB (0.8%), 0% eff. + moz_places_metadata_snapshots_extra_typeindex: 32KiB (0.8%), 0% eff. + moz_places_url_hashindex: 96KiB (2.5%), 52.1% eff. + moz_places_frecencyindex: 96KiB (2.5%), 33.8% eff. + moz_places_lastvisitdateindex: 96KiB (2.5%), 59.5% eff. + moz_places_originidindex: 96KiB (2.5%), 35% eff. + moz_historyvisits_fromindex: 96KiB (2.5%), 57% eff. + moz_places_hostindex: 128KiB (3.4%), 69.8% eff. + moz_places_guid_uniqueindex: 128KiB (3.4%), 55.8% eff. + moz_historyvisits_dateindex: 128KiB (3.4%), 72.4% eff. + moz_historyvisits_placedateindex: 160KiB (4.2%), 68.4% eff. + moz_historyvisits: 192KiB (5.1%), 71.5% eff. + moz_places: 1248KiB (33.1%), 94.8% eff. > Task: _refreshUI

Accessibility

well, just kept pressing the tab and all bookmarks cleared for good, just need to reload and organise!