I keep getting the following when running KJFK V2's install.
That's not really an error, is saying it can't DELETE an old AFCAD for LSGG. It can't delete it, because you don't have it, apparently so, there's nothing to delete, it's just a cosmetic error, and I believe it should be fixed in the JFK v2.1 installer or the current Stand-Alone Addon Manager installer, that doesn't give that message if there's nothing to delete.
In any case, be sure you use the current JFK installer, which is 2.1
Why is it messing with Geneva's (LSGG) airport file(s)?.
It's not "messing", it was trying to *fix* a potential problem with AFCAD duplicates, and fact that all our installers update all our AFCADs is very well known and has been like this for more than 1 year, since GSX was released.
They obviously do a *backup* of your existing file, in case you modified it so no, nothing is really messing your files.ù
I have two VIRTUALI Addon Manager X in my (Install / Uninstall Programs) listing
That's not a problem. Either you have FSX and Prepar3D installer, or you removed something manually and reinstalled it. In any case, it's not an issue, and opposite of what most people believe, that doesn't always mean you have installed two copies of a program, it might just mean you have two Uninstallers, which happens if you removed something manually, or a too aggressive registry cleaner utility did that.
Even if you install anything from us multiple times, only one copy will ever run.