Li-po $100.00 question

OK for now, i'am runing 2x Thunder Power 5000mAh, 3s, connected in serie, in my e-revo.
BUT, due to the MMM failure, i'll probably put the e-revo on the shelf and run my Slash to the place, with my TP batterie.
SO here's my question: If i run my pack separatly in my Slash, and take care to run each pack the same amount of cycle (one run on pack "A" and one run on pack "B".....etc), and i charge/balance it togheter every time, is i'll can re-use this pack togheter in serie in my revo in the futur, when a solid controller will be available to put in my e-revo????

Or the fact to run the pack separatly during a "X" amount of time will not permit me to re-utilise them togheter later??

Thank you