Originally reported in https://translatewiki.net/wiki/Thread:Support/FuzzyBot_imports_already_fuzzied. (the period is part of the URL, but Phabricator ignores it).
My guess is that $handle->isValid() in TranslateEditAddons::onSave might return false and we skip adding fuzzy/transver tags and also updating stats. It's not clear whether this is a duplicate of T224112: MessageIndex is not updated after running autoimport or a separate issue.
We can either test this manually after the above bug is fixed, or add logging to see when this happens if it happens.
Stats will heal themselves automatically, transver tags are lost (maybe not a big thing, as semantically we don't know), and fuzzy state can be fixed with populateFuzzy.php script, which is currently broken.