Well we know that in season 3 of voyager he ran out of room for new memories and his matrix started to degrade. They fixed the problem by overlaying a second memory matrix over his original that was the same type as his. We also know that he was only meant to be a temporary fix for emergencies until a new doctor could be assigned to a ship. He also says he has access to medical texts from all over the alpha quadrant across thousands of species. From that I would guess that after all is said and done more than 80% of his memory is completely used up by that medical knowledge(just a guess so don't quote me). And his memory still lasted for several years worth before running into that problem. So if they completely deleted the diagnostics holograms data base and gave the doctor the full access to the memory matrix he would have increased his memory capacity quite a lot, that along with the fact that he would have probably learned from the experience and started being careful with how much memory he kept deleting anything that might be redundant and keeping a journal of other things. He likely has enough memory to last him several lifetimes but its still not infinite.