A registry problem mainly with payware add-ons, but a Registry Repair Tool from Flight1.com - Flight Simulator Add-ons for FSX and Prepar3D will sort it out.
I'm running 2x versions of FS2004 & P3D from a 2TB portable drive, as my laptop's SSD is only 500GB.
I also have a spare 'vanilla' FS2004 install on the drive for backups, and also if I decide to have another install.
For possible Registry issues, as some installations look for FS2004's default install, I have a FS2004 install in it's default install folder, with ONLY the FS9.exe in it, nothing else. Then I just copy & paste from there, to my D:\ drive, where the sims actually sit.
So far, I've been running the sims of the portable drive, thats permanently plugged in to my laptop, for 2 years, now, with no issues at all, maybe a very slight delay in selecting planes or scenery.