Registration/normalization with subj in/out of scanner in

Can you point me in the direction of where your team has answered what I think must be a common question:

how do you handle registration/normalization if someone gets out of the scanner and then back in?

Meaning–subject does structural scan and 3 runs of fMRI task; has to get out to use bathroom; gets back in to finish other 3 runs and we do a 2nd structural scan just to have it.

When I preprocess data with–how do I handle fact that they got out of the scanner (clearly moved for runs 4-6 vs runs 1-3)?

Not sure if (a) using the giant move option takes care of this with the original structural scan?

Or (b) if I need to first register runs 1-3 with structural scan #1, register run 4-6 with structural scan #2, and then concatenate?

If (b)–how?

Naively–feel like you must have answered this in handouts somewhere or on the message board–b/c it is a common occurrence.