I am just winding up my first cold and congestion experience. While I didn't get numbers quite as bad as you, yeah, everything (AHI, VS, leaks...) went up. I felt almost as bad in the mornings as I did before I started on CPAP. It's going back to normal now, slowly but surely. Hang in there.

Both Encore Pro and MyEncore seem to run fine without it being active. Is there any reason why I can't remove it from my startup list? The short answer is no, there's no harm in removing it from your start up folder. The long version is what you are seeing when your OS starts is just the SQL Server...