Now that you're familiar with basic nature of EFI Service Partition, you can set aside a copy of your Clover EFI. The tools you need to work with ESP are present in every system.
If your Clover EFI was in the ESP for the Windows drive, then don't do that, keep it in the Mac drive ESP.
If Windows Recovery reached into the ESP in another drive, when/how does this happens? Sounds unlikely, but maybe NVRAM state comes into play in some subtle way for Windows Recovery? Idk.
Obviously if you disconnect Mac drive then Windows Recovery can't pollute it.
As to backups, the problem you had is beyond the scope of any OS-level backup tools. You have to learn the approach to multi-boot config mgmt that fits your config and be aware of edges between BIOS, EFI and OS.
* * *
- Doctor! It hurts when I do this.
- Don't do that.
- Will I be able to play the piano after I recover?
- I don't see why not...
- Great, I couldn't play the piano before!