Hi ajilen,
I had the same problem with my Pixel. To be honest I don't know if I've even completely fixed it, but rather, found a workaround to it. I'm assuming that when this timeout happens, if you look at your Pixel in My PC, it doesn't show the "Internal shared storage" drive that is usually there? I do think this is ultimately a Windows problem, and not MusicBee.
I did a good chunk of research, it's happened to other people. Some suggested using a USB 2.0 port instead of USB 3.0. I tried both a USB 2.0 and 3.1 port and these both still had the same issue. Some suggested using a different brand cable (but I didn't have any other USB C cables so couldn't try this).
Ultimately I then did 2 things, and either of these made it work (I wasn't in the mood for scientific testing haha)
1.) I checked for updates to some drivers, and I updated a handful of USB drivers that were available.
2.) I staggered how many songs I sent in one connection session. I use one "Mobile Sync" playlist, and then top played, recently added, etc. I filled up half of my playlist, synced (and this worked, because after 85 songs or so it didn't timeout) and then I finished the playlist, reconnected, and synced.
*I used a 3.0 port for this successful sync.
I figure going forward I'll be ok, because I won't be syncing more than probably 75 tracks at a time at maximum, assuming I don't go too long without syncing. I know it's a band-aid rather than a permanent fix, but it got the music on my phone and I've been able to sync 2-3 times already with no problem.
Ultimately I don't know if this is a Windows problem, or a Windows/Pixel or Portable device compatibility problem. My USB 3.0 external HDD for backups never gets disconnected from my PC and has never had the problem.