Cannot turn off FileVault process in terminal or DU in macOS High Sierra
If you're on a laptop, make sure it's plugged in as FileVault will pause on battery.  If that's not causing it, you can create a clone of your system using Carbon Copy Cloner (http://www.bombich.com/) or SuperDuper - that's what I would do - and then wipe the system, re-install the OS (High Sierra isn't that bad).  Then I would enable FileVault on the clean system, wait for it to finish encrypting what little is there (OS only, a few gigs), then restore your files from the clone manually, then enable Time Machine and have it do its backups.