My rules for moving/installing aircraft into P3D_V4:
1) If it is a P3D_V4 compiled Aircraft. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Good to go
2) If it is a P3D compiled aircraft and has no 32bit "dll" that would require replacement. . .Good to go
3) If you have a "Native FSX" aircraft (no 32bit dll's and no "gau or dll" gauges). . . .Good to go
4) If you have a "Native FSX" aircraft that relies solely on gau or dll gauges or a mixture of the two. . .your discretion, but gauges will not display
5) If you try to push an FS9 aircraft that is considered "FSX Compatible" into V4. . . .forgetaboutit
It is my personal view that none of these, most certainly items 1 thru 4, will damage the Sim in the sense that you would be faced with a complete reinstall of the Sim. You may get a "lockup". . .you may get a CTD (but I doubt it). . . but I've gotten those before when trying to load Sim-specific aircraft. Even item 5, wont damage the Sim. It might not load, it might load with no wings, no landing gears, opaque windscreens or no textures. . .but it won't damage the Sim in the way I think of the Sim being "damaged". I've never had to reinstall a Sim because an airplane was incompatible.
This info is what I've found to be true on my systems (and I've had at least 6 since Pro Pilot). I do stupid crap all the time (this latest debacle is proof of that). . .I've had to reinstall Operating Systems, I've had to reinstall Sims more times than I care to think about and I turn right around and do the same stupid stuff all over again, but in all those years with all those mistakes, not once have I seen a Sim go down and need to be reinstalled because of an incompatible airplane and I use the very technique I posted above whenever the installer allows.