Do re-runs count as report credits?

Yes.

Re-runs using the Update Score option consume 1 POP Credit.

Re-runs using Switch Setups or Make Changes consume 2 POP Credits because a fresh report is generated.

To avoid unnecessary credit usage while editing, POP recommends using the Chrome Extension or the POP Content Editor. Both let you check page scores and important-term counts while making changes without consuming a POP Credit for every check.