Whether the new ones overwrite the old ones is a matter of chance, but you can recover the deleted ones the same as you can recover any deleted files - an app like
DiskDigger undelete. (t will take the paid version to undelete a .crypt file.) The phone has to be rooted (to undelete any file - even programs that claim to do it with unrooted phones first root the phone, then undelete the file, then sort of unroot the phone - but when you try to get an update, you may find that it fails, because there are still traces of the phone having been rooted). And, since WhatsApp is running, you'll have to undelete the deleted files to slightly different names, freeze WhatsApp, delete the new files and rename the old files back to what they should be. Then unfreeze WhatsApp and you should be good. (
Link2SD will take care of the freezing and unfreezing, and it's free.)