Yes, MP3 (lossy) is lower quality than FLAC (lossless). It will depend on what settings you used for MP3 in how much you'd experience this quality loss (ie. 320kbps MP3 would generally sound the same for most people).

Did you enable Volume Leveling in the Auto-Conversion settings?

I had my phone set up the way I wanted it for several years so that when connected to my truck's Uconnect via BT it would keep all sources (radio, MMA, etc) at essentially the same volume (when switching from radio to MMA I would not typically have to worry about reducing the volume to avoid blowing a speaker).

I recently had to resync my entire library and switched from FLAC to MP3 format on the microSD card. During this process, I must have changed a setting either on MMW or MMA such that now the tracks played through MMA are very quiet and I have to dramatically increase the volume to hear them. I'm not an audiophile, but it also appears that the fidelity is dramatically lower now too. The lower quality could be related to the format change I suppose, but I would like to figure out how to get the volume leveling set up again.

I have the volume leveling enabled on MMW and all tracks have been analyzed. I have "Level volume" enabled on MMA. I don't recall if there was a setting where the FLAC was reencoded with leveled volumes but that's not something I would have intentionally enabled if it's even possible (I prefer to have clean source tracks and any adjustments made during playback). Is there some other setting I should be looking for?