I have about 10 months left on my Non-B visa and will apply for a temporary work permit to set up a BOI company.

This temporary work permit will be valid for about 3 months.

I need to do a visa run during this time because my first 90 days entry will be up soon.

So will the work permit still be valid when I come back to Thailand? (Of course still within the original validity).

Cheers

Yes, a work permit is to permit work, doesn't have anything to do with immigration.