Ill create a "rollback" option in the next release. Good Idea.
The only things that are changed by the program are the following keys in the mis files:
Fog=0
FogRand=0
Clouds=1
CloudsRand=1
Precip=1
PrecipRand=1
WindHeading=191
WindSpeed=0
WindRand=1
WeatherRndInterval=11
Those are not stock values shown there, someone may have the stock values that you can go in and change back manually.
Those are the ONLY values that SH3WeatherGen touches... it does not add textures, or any files... it ONLY modifies those values directly in the mis files... it does not overwrite anything or copy over anything.
As for the black sky problem you are reporting... no-one has ever reported this to me, nor have I ever encounted this problem myself, and I use it all the time....
Possibly, have you installed any sky mods lately? What mods do you have installed through JSGME and I will try to reproduce your problem.
PS- Which version are you using? can you get the contents of the log file for me (just open it in notepad and cut and paste the text here), if I have a faulty section of code I will happily fix it.
I also need more information:
Are you using random or manual weather?
What month did you have selected?
Did you have the 29th Flotilla option checked or not?
I can fix most issues if you can detail the problem for me....
Cheers,
Jamie