Duck Swapper - 2019-11-26

I've just started using VeraCrypt and used it to encrypt my system drive with no problems - however, I wanted to also do this to my main storage drive, on which the system does not reside. However, every time I try to do it, I get informed that it cannot be dismounted and whether I want to force dismount - which I agree to but still, I just get an error reading that it failed.

I've read some tips online and some of them recommended unchecking Windows's file indexing on that drive which I did but it didn't help at all. I have a hunch that the problem lies in a weird interdependence between the drives in my case - the "system" drive basically holds only the system and the things that would benefit from being on an SSD; the partition I'm trying to encrypt, however, holds a lot of other programs (some of which are probably running in the background) and symbolic links from the system drive point to some of the places there, too. Thus, it's basically impossible to run my system without anything from this drive running. I also have yet another storage drive - which does not host any programs and links unlike the problematic one - and that one got encrypted with no issues whatsoever.

What should I do in this case? Can I somehow encrypt it without running the full system - like from some command line without the need to run Windows itself or in safe mode? How should I progress in this case if I'd like to encrypt the drive in place?