It shouldn't be problematic to convert any stems from 44.1 to 48k. As for quality, I guess thats subjective but I really cannot hear a difference between 44.1 and 48k personally, though I have never done a live recording in 48k and then in 44.1 and compared them. Bit rate is WAY more important than sample rate, so make sure you are recording at least in 24-bit (32-float if your DAW can do it).
I choose my sample rates based on what the final output will be. If I'm writing for CD, then I record in 44.1. If I'm writing for film, I record in 48k. This is just so I dont have to convert it later. Seeing as how you have already started in 44.1, you can either finish in 44.1 and convert the files when you are done (that way you are assured everything you have done so far will be correct) or you can switch to 48k and go from there. In theory you should be able to switch your DAW from 44.1 to 48k and everything should play back correctly.
So you have a choice of staying with 44.1 and converting all audio to 48k before you record (I would for sure record live players in your final delivery sample rate), going back and switching your 44.1 projects to 48k and rebounce, or having a mix of both 44.1 and 48k cues. I personally, knowing that you will be recording live musicians, would switch all cues to 48k. I would bounce out an audio file for all cues have finished, convert the project to 48k, import the 44.1 audio bounce you did previously (making sure its converted to 48k when importing) and A/B the two and see if anything changed or sounds different. Once its ok save the 48k version and keep working. Again, in theory switching sample rate mid project (as long as all recorded audio is converted) your project should sound and function the same. In fact I just did a test switching my DAW from 44.1 to 48k with VE pro connected and it switched just fine. The only think you have to double check is audio files in your project, as they may or may not be converted when you change sample rates depending on the preferences you have selected in your DAW.
Hope that helps.