I made a bug report at vkd3d-proton and the author suggested to run wine with the option VKD3D_CONFIG=force_raw_va_cbv
This allows me to run the game both on the newest vkd3d-proton 2.14.1 as well as on my older yet unchanged wine prefixes from before the Eve patch that run vkd3d-proton 2.11.1
So i run Eve with wine now like this:
env WINEPREFIX=“/home/user/.wine” WINEESYNC=0 WINEFSYNC=0 VKD3D_CONFIG=force_raw_va_cbv wine C:\users\user\AppData\Local\eve-online\eve-online.exe