neither updating Firefox nor updating Greasemonkey should delete any userscripts. Does "deleted" mean they don't appear in the list anymore or are their entries there but the source says "This script has been deleted"?
The latter is something some script-hosting pages do when they detect that a script is malicious and should be removed. They will replace the content of the script and through auto-updating the script content gets overwritten with the new content consisting only of the comment that the script was deleted. This is however not something Firefox or Greasemonkey have any control over.
To prevent that you can disable automated script updating, or you can create and load backups from the Monkeymenu using the Export and Import menu items. If you haven't done that, I'm not 100% sure but I don't think the script database from Greasemonkey is versioned. If that assumption is wrong, maybe Anthony Lieuallen as Developer can chime in. Maybe the source site you originally got the script from offers access to older versions.
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