I suffered from that same issue for a long time and just stopped trying to change aircraft in flight, I only changed when on the ground. I never went as far as re-installing as that just seemed like a lot of effort for a temporary result. I retired from active flight-simming due to burn-out and life changes for about 18 months and when I came back just a few weeks ago I realized virtually all of my ancillary programs were out of date and needed updating. Things like Little Nav Map, Active Sky, Join FS, Teamspeak 3, Nvidia drivers etc. were all way out of date so I set about updating them all. The only thing I didn't update was the sim itself.
After such a long time away my controllers were a bit reluctant to perform correctly, hampered in part by a new puppy actively chewing through the cables on my rudder pedals and my keyboard! I was able to rewire the pedals and bought a replacement keyboard in the Prime Day sales which fixed those issues but once I got back into the sim I started to notice intermittent problems with buttons and axes on the throttle half of my X56 HOTAS system. These became so bad that I made the decision to replace the throttle section (the stick is still working just fine) and after a lot of research and talking to other SOH members on the SOH Teamspeak channel I bought a pair of Logitech/Saitek USB throttle quadrants. At some point I must have started the sim without any controllers connected which messed up the controller config settings and I had to write a new one for the new throttles anyway. I use the full version of FSUIPC (which also got updated) to set up my controls as there were always issues trying to set up the X55/X56 controllers in Windows 10 64 bit when using the Logitech provided software or the sim controller section directly.
After all these changes I started flying again and one day, for some unknown reason, I had a need to change aircraft in flight and fully expecting a crash I went ahead and switched aircraft. Lo and behold I was able to swap aircraft without the sim locking up or going into a CTD! I was so amazed I did it again, several times, to make sure it wasn't a fluke! Bottom line is I don't know what fixed my system as I changed so many things in a short space of time but something obviously fixed the issue but I do know for certain that RE-INSTALLING FSX IS NOT THE FIX AS THAT IS THE ONE THING I DID NOT CHANGE!
Make sure all your ancillary programs/tools/modules are up to date and I would suggest re-doing all your controller configs too. As I say, I don't know specifically what fixed the problem but something did and it wasn't re-installing the sim (that is always a last resort for me). Good luck and let us know if you find a fix for your particular system.