Absolutely no problem. In the passport that I just retired, I had an Indian multi-year visa first, then got a Pakistan visa, then got a second Indian multi. Neither country cared about the presence of the other's visa in my passport, either at the consulate or when I arrived. I have also traveled via Pakistan Airlines from Karachi directly to Mumbai--it would be pretty tough for either government to make a stink given that there are direct flights between the two countries.