A deep discharge definitely makes its mark on batteries. Their capacity will be reduced, but you'll have to recharge them to find out whether you can tell the difference. At this point what's done is done, so you might as well recharge them and use them like normal to find out whether (how much) they're still good.
What size batteries are we talking about here? If they're, say, 200 AH then a 4 amp charger should take many days to get the job done (like all week, perhaps). You should really think about getting a bigger charger.
The first 70% or so of charging is called "bulk" and can go fast (if the charger is capable). In the remainder of the charge cycle the current tapers down, so the final part just takes a long time no matter what. At this point the bulk is probably mostly done, so a bigger charger might not do much for you now.