if Amiga boots to 640x256 then something must have happened on Amiga side. You shouldn't be able to break it with WinUAE settings. But who knows. Especially if it works via remote desktop. Strange.
Anyway, you can always reset the screen mode on Amiga side. Boot or reboot AmiKit and hold down both mouse buttons to get to Early Startup menu. Select Boot with no startup-sequence. Then type the following commands to reset your Amiga screenmode in AmiKit (if successful, AmiKit will ask you to select new screenmode on next reboot).Delete SYS:Prefs/Env-Archive/Sys/screenmode.prefs
Also, it would be best if you could restore the original AmiKit config for WinUAE too. To do so, use Windows to go to the folder where you installed AmiKit, and delete "AmiKit.uae" file located in WinUAE/Configurations folder. Then clone "AmiKit-windowed.uae
" file and rename it "AmiKit.uae
Btw. if you make changes to WinUAE settings later, make sure to save them this way: In WinUAE go to Configurations tab, mark the "AmiKit (Default configuration)" entry and click SAVE button. This way the changes will be saved to AmiKit.uae file which is always loaded by AmiKit Launcher - as you correctly presumed.
Well, ff you haven't customized your AmiKit much, maybe the fastest solution would be to re-install AmiKit from scratch
If you do so, backup AmiKit/AmiKit.hdf so in future you can only replace this file to get back to AmiKit defaults. You can also backup that file before you install something new to AmiKit or just before you want to experiment with AmiKit a bit
Hope it helps.