time machine remembers moved or dead drives

Hello. I've been having a hard time wording this in typical searches, to get appropriate answers.

Here goes: I have a older Mac Pro with four internal drives. One drive, my boot drive, failed.

I had been using an external drive for my Time Machine backup. On that backup, I had included a lot from the other internals.

Once I had isolated the problem (the internal was dead or dying) I made room on one of the other internals by moving things around- condensing to allow for a Restore to one of those three remaining drives, temporarily, as I planned to buy a new internal and a larger external.

Suprisingly, it went great! I ended up with a perfectly restored boot drive with all my Apps, etc.

Now the problem:

When I turned Time Machine on, intending to create a newly restored version of my boot drive---to the new drive I just purchased, TM had a stored list of items that were spread out among the other drives, but I had moved these items all around.

I'm afraid to run TM at all now, not knowing how to tell it to ignore items, volumes, even drives; and restore only the boot drive with its applications etc., and not the various other items that were in places that no longer exist.

If this makes sense, and anyone can advise me, I will greatly appreciate it.