Could you check About on Duplicati’s main screen to get the version of Duplicati? As a long shot, there was a change in 2.0.3.10 – " Removed automatic attempts to rebuild dblock files as it is slow and rarely finds all the missing pieces (can be enabled with --rebuild-missing-dblock-files ).". The log looks like it created the missing block list, and an older Duplicati might be going through local and remote files trying to recreate a dblock.
There’s also a recent issue Purge Broken Files Running for 36 Hours where things stalled so tightly that strace wasn’t even showing system calls. Mono was updated just in case it helped, but it didn’t help this problem. Possibly you could try strace, ltrace, sar, and other tools to look beyond just CPU and memory.