Thanks for the comments everyone. I feel better knowing it was not just me who felt the removal of the main drain was a bad idea. That almost makes me want to forget using this guy to begin with. His price of $2500 is below a few other quotes we have received ($2800 and $3000).

Only one quote mentioned patching the floor if needed (up to 5 sf is included). 5 SF is nothing.

These are additional questions I will now be able to ask, thanks to you guys. I generally do all work when it comes to my house, including electric, plumbing, roofing, etc. and hate it when I need a professional to come do something I do not have much knowledge or experience doing.

For instance, the first guy that came out looked at the pool and when I was telling him about the liner history and what we were looking for, he kind of just ignored me and asked where the filter was. When I showed it to him he immediately said the valves are old and should be replaced and moved closer to the pool. That just made me feel like he was looking to make money somewhere else than just a liner replacement.