PROFILE IN A LOOP

It depends on the scan settings. 

If you have anything other than FIND NOMS for your Nominals Method, it compares the new nominals of each scan to the measured result of the last scan (or first scan with MASTER selected), regardless of CAD.

If you have anything other than DEFINED for your Exec Controls, your actual hits are reflective of whatever your scanning sensor produces (instead of the hit/spacing you defined on CAD).

There's other knobs within scanning that can impact your answer i'm sure.

Click F1 within the scan menu and get reading. dig into the blue text links for each setting, so you can gain a better understanding of the intricacies of them.

Legacy or Xact/Geo Tol?

I know with Xact and Geo Tol, I had to do a flow control print command (depending on loop #1 vs loop #2+ to write then append) to delete instances after each loop, as Xact and Geo Tol hosed my dimensions in the report if I did not. 

I know I found an issue with looping scans and reporting profile in the standard looping found in PC-DMIS and created a work around: nexus.hexagon.com/.../closed-loop-scans-and-looping

If you're using Find Nominals, then yes, it will compare against the CAD surface it was defined on.

If you're looping parts (rather than features on a part) there's a technique you can use to make sure the model moves with the part.  The standard LOOP command doesn't work in this instance.

Use a do/until loop and recall external alignments for each fixture station, then saving them as curr.aln, then recall curr.aln before the part measurement.

That sounds like waaaaaay too much work. 

It's like anything, once you've done it a couple of times it's quite straight forward, or you can copy-paste a previous program (and simply edit where necessary).