Have you tried booting Clover via USB and seeing if it shows your Mac OS partition?
I haven't updated Clover on USB since High Sierra and yet it shows my current APFS Mac OS partition.
If booting off your USB into Clover, and it only shows Windows partitions let me know.
Have a look at my...
When you updated to Mojave it probably switched your HD from using the HFS+ file system to APFS.
What this means is you probably don’t have the required kexts in Clover nor on the HD itself.
So the first thing is you need a bootable flash/usb drive that has the Mac OS installer on it. Boot...
So I updated to Mojave via App Store once it was officially released.
After doing so Clover would not detect my drive. This was due to switching from HFS+ to APFS and not having the required kexts.
I downloaded and installed the latest Clover from here: Clover UEFI Boot Mode with Emulated NVRAM...
I followed the 10.13 High Sierra guide. After I installed macos 10.13, I used Multibeast to install Clover and Fakesmc only with the quickstart UEFI only option. I didn't check any additional kexts. When I boot without usb I get the following in the picture attached. I can boot successfully with...
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