Nothing in the new FSDT installer can have cause any problems with your already installed products.
In fact, the major advantage of this new installation system (which is the officially supported one), it's precisely that, we now our own private configuration files, and we DO NOT have to touch ANY of the core Prepar3d configuration files anymore.
So, this system is inherently safer than the previous one so, whatever happened to you other addons, it surely hasn't been caused by our installer.
UNLESS, one of your configuration files (like the scenery.cfg, the DLL.XML, or the EXE.XML or the Prepar3d.cfg ) was ALREADY corrupted or with a syntax error BEFORE you started the installer.
Because, even if we won't ever need to interact with these files anymore in the future, the migration process had to *remove* all our stuff from such files. Which of course, is no different than we already did we you Uninstalled any of our products so, if you had a problem with your existing files (not legal XML, not legal .CFG, etc.) they might have caused this problem, same as if you were uninstalling normally.
But of course, is not possible to say for sure, without checking your system. I'm available for a Teamviewer session, if you want, and I can fix this in 5 minutes. PM-me to arrange this.