I downloaded a new scenery that apparently requires SODE 1.6.5. I noticed that my FSDreamTeam GSX apps use SODE 1.6.3.
No, it doesn't.
The current GSX installer comes with SODE 1.6.7, and before that, it came with 1.6.5 so, if you had 1.6.3 installed, you just download the latest SODE INSTALLER ( SODE it's updated with the installer, not with the configurator ) and install it.
There are no problems updating SODE and, in fact, it's always best to always use the latest version.