First thing. Always keep the old version under its name, example - if the latest version is 17, first rename the last one to WHDLOAD16_9 and keep the latest one under the name WHDLOAD.
Now, unless you don't have WHDLOAD in PROGDIR: of the game, your games should always use WHDLOAD which is in C:. If you think that the latest version works incorrect, then just rename the default tooltype of the game that crashes or does not work and use C:WHDLOAD16_9 (or any other of your choice and backup you have) instead of WHDLOAD. There is no way that going back to the previous "working" version creates issues that existed when using the latest one.
About the keyfile - make sure you have it in L: or/and S: or/and C: location. Try also checking WHDLOAD prefs in case there is some strange PATH written in which WHDLOAD is looking for keyfile (but I doubt it) or that makes something strange going on.
If all that fails, there is always a virus option in your system that simply changed something in some files (maybe even altered the keyfile and it is not recognisable).
