In theory, any permanent change to the wav data will have an effect on sound quality. In practice, going from WAV to FLAC, it's probably not anything that anyone would hear.
That said, I wouldn't do any permanent adjustment of volume unless I absolutely had to. I like to leave my lossless files as unmolested as possible, and changing them in ways that can't be undone goes against that. I want those files to be the source they came from exactly.
As far as the server and replaygain, I think that's more a function of what you're going to be using to play back the files from the server. If the tags are in the files and the tags are read by the program rendering the output, you shouldn't have a problem. Finding players that can interface with your server and read replaygain is what you should be researching IMO.