@mascotca I have a healthy respect for paranoia. Indeed I create and work on all projects directly in Boxcryptor, which continuously syncs with Dropbox and thus implies various degrees of worst-case backup depending on your Dropbox settings.
You may be able to improve your workflow by going to Boxcryptor–Preferences–>Advanced and enabling the Enable Trash option. In cases where I fear a problem that might result from version deletion, even with the buffer of Trash, I create a subfolder called “x” and move old versions there, never to be deleted.
It is annoying that Spotlight does not work, but as Boxcryptor says they will fix that. If your work relies heavily on automated searches it seems like DEVONthink offers more than Spotlight. The question is whether searching all the time is a good way of working.
I think @LucB might argue that search is a machine, rather than human, process. It seems a lot harder to teach the machine the relationship between “surfing.jpg” and “Denise.pdf,” so that it retrieves those in searches, than it is to just Hook those together once and then invoke Hook and see them every time thereafter. Nor does your mind, when it remembers surfing with Denise, need to flip through every Denise you’ve ever heard of, the films of Bruce Brown, and the Beach Boys.
I find that creating my own associations with Hook often produces better signal-to-noise than brute-force searches, which generate a lot of meaningless results. In this way I find Hook to be a better tool, for many kinds of work with ones proprietary stuff, than search.