MacOS – Deleting all user data from Time Machine after backing to disk

Your best bet is to turn off Time Machine, eject the backup drive and get some help from someone trained to know what Time Machine looks like.

It's entirely possible, the software deleted the old files and over-wrote them with new backups. It's also possible you had a minor glitch in the permissions and all is well.

Assuming you are near a retail store, you can usually get a quick read from someone in the store or worst case, make a support request at the bar. Phone support is also an option, but I've found that taking the backup drive and the mac (as well as your old mac drive / CPU) in to the store is the fastest way to get someone seeing exactly what is going on and your data uncertainty sorted.

As much as I like to help guide people, it's really best to disconnect the drives and reduce the risk of more files getting deleted and not learn on this one instance if you can get some professional help on this.

I believe this is a staleness prevention. That whenever there is too long between backups Time Machine uses a more thorough way to ensure that the backup is complete.

It is my understanding that the 40 GB is a "this is how much we consider for backing up" and that the actual data transferred may prove to be a lot less if the files turned out to still be identical.

Based on your description I believe that you have reached a point where you need to let your Time Machine backup catch up - work on its own until it is done, if at all possible. If you cannot wait for that, perhaps now is a good time to buy a new drive and use that instead and have the old drive as a backup backup.