You have some strangeness (and wrongness) in your question. Time for a little education (my >15 years of CE app dev occasionally pays off).
As far as versioning goes, Windows CE and the Compact Framework are totally unrelated. Well, there's some "X supports Y" sort of stuff, but otherwise they are unrelated.
Windows CE 2.0 dates to 1998 or 1999. At that point the CF didn't exist, it was eVB. You are not running CE 2.0. I guarantee it.
For the Compact Framework, there are 4 major versions, with some service packs for each.
- CF 1.0 - Released with Studio 2003. Not seen much past CE 5.0 days since CF 2.0 was released while CE 5.0 was in the field.
- CF 2.0 - Released with Studio 2005. This one is pretty common in older handhelds running CE 5.0 and CE 6.0
- CF 3.5 - Released with Studio 2008. This one is somewhat common in newer hardware. It can be installed on a lot of older hardware.
- CF 3.9 - Released with Studio 2012. Only works on WEC2013.
If you have a device that's reporting CF 1.0, then it can only run an app built for 1.0. Support for building for CF 1.0 apps ended with Studio 2005. You may be able to install a newer version of the CF (via CAB file) if the hardware has space and memory for it.
If you have a device reporting CF 2.0, it can run CF 1.0 or CF 2.0 apps. Again, you may be able to update to 3.5 if you have space and memory.
If you have a device reporting CF 3.5, it can run CF 2.0 apps (and probably 1.0 apps, though I doubt I've tried that in a decade).
You cannot remove any version of the CF in ROM. You can, however, install side-by-side. Installing an older version is generally not recommended nor necessary since newer versions of the CF will run apps built for older versions.
Occcasionally you may find that a device with CF 3.5 cannot run a 2.0 app. There were a couple compatibility weirdness things. In those cases you can force the CF 3.5 to actually run in 2.0 mode (without having to install the 2.0 bits) by modifying your app.config file and explicitly setting the SupportedRuntime. Take a look at this MSDN page.