Hi.
Cryptomator does not support Dokany Version 2.x. Only versions 1.x.
Maybe some other software installed a dokany version 2.x on your system? To check this please go to windows settings and search for dokany in the list of installed software. If there is a version 2.x installed, you should find out what has installed this. If you are sure no other software needs dokany 2, you can just uninstall it and install the latest 1.x version.
Cryptomator does not switch settings during an update. There are people out there who prefer Dokany 1.x or even WebDAV as virtual file system.
So Cryptomator does support 3 virtual file systems. WebDAV, dokany 1x and Fuse (WinFSP)