Warning message after doing backup in TWRP on Honor 8 (FRD-L09)
To isolate the problem, 1) reboot into Android and see if it does so properly, and 2) reboot back into recovery and do the same operations.

Judging from your response on the 2 points, it seems your recovery is at fault here. Not unmounting /system is usually not a problem: that step is done as a safety precaution to prevent accidental modification to /system when not flashing. As long as you don't do that yourself you should be fine.