I had a similar problem. When I deleted the previous backup and started over, only the most recently updated places were backed up in the place directory.
Oh dear! Can you retrieve that deleted backup? It’s always a good idea to keep at least … well the rule is 3 copies of backups (the 3-2-1 rule), but minimum 2.
Anyway, if the new backup is missing some older data, you can often trigger minor changes to the data by browsing back through the timeline view by day. That will then mark those items as due for backup again. Though for Place files… that’s more difficult. Those will only get marked as due for backup if the Place has changed in some way, which typically only happens when being assigned to a Visit. Hmm…
Unfortunately I can’t think of a good way to get places marked for backup again. Starting a fresh backup (turning backups off and then back on) should mark everything as due for backup, but that’s actually quite a long/slow process (it needs to update every row in the entire database), so there’s risk of it not completing if it’s a large database. Which is probably what happened in this case.
I would say do the swiping back through days in timeline view, to at least mark all the timeline items as due for backup. Then possibly that will help fill in some missing Place files too.