Dead ball fouls prior to the snap

[kentref]

Subvarsity game yesterday. Team B has 11 on the field and B11 goes off the field and then re-enters prior to the snap.
Just after B11 re-enters the field of play, the HL tosses his flag for a false start on Team A.
As R, I tossed my flag upon seeing B11 re-enter. My whistle unfortunately did not come before my HL had tossed his flag.
3 man mechanics - I (as R) was counting B, that's why I was paying attention to B11.

I shut down the play and after talking with my HL, enforced only the penalty against B for illegal substitution. My rationale was that that foul occurred prior to the false start and I was shutting the play down before the false start occurred, even though my whistle technically didn't sound before the HL tossed his flag for the Team A false start.

Did I handle this correctly? Thoughts, comments?