I really wouldn't advise doing anything at all. The lime in the mix ensures there is enough calcium. The BER is the result of some other factor, quite possibly weather related. It will almost certainly clear itself soon. The afflicted fruit won't improve, but the BER will simply stop appearing on new ones.

If you feel you must add lime then do not add it to the water reservoir unless it is hydrated lime rather than dolomitic (which is what was added to the mix). Be very careful with it and use a really small amount (like a teaspoon) as it is very potent stuff and will radically shift pH.

I don't recomend anything more than a wait and see approach, however. BER is very common with tomatos no matter how well cared for and most of the time it clears itself with no intervention.