Mike_tyke21,

As far as I know if one does not use complete 6 yrs of H1, s/he is cap exempted next time they reapply for H1 (As of current rule, never know what it will be in future). In your case next time you apply/activate your H1 you should be getting max for 3.5 yrs but it depends on immigration officer that has your petition and the type/length of your job. But it is must to have sponsor to re-apply for H1B after you finish your masters.

But how wise it was to move from immigrant visa (H1B) - non-immigrant visa (F1)? Are you sure that after completing your masters you will have employer to sponsor you? I hope you have solid plan to get back to H1. If you have a plan to stay here for long time, you should have started GC processing not other way. You could go for masters any time but getting H1 and moving to GC going to be difficult with current situation. I wish you good luck for your grad school.

P.S: Above is not legal advice, just my opinions.