The COMPACT command describes three configuration options that are currently available for tweaks.
Compact - Limited / Partial suggested an algorithm change. Reply was a half-done idea that –threshold documentation and code look like it’s used two ways. Using separate controls might give better control, however with a more complex UI. Someone could take a closer look at the compact code than I took…
threshold
--threshold = 25
As files are changed, some data stored at the remote destination may not be required. This option controls how much wasted space the destination can contain before being reclaimed. This value is a percentage used on each volume and the total storage.
For the time being, though, lowering --threshold in search of more-often-but-smaller compacts may help.
Small increments (adding files as you go) also does better, if an error occurs somewhere along the way.
Choosing sizes in Duplicati would be worth reading. For a backup that large, larger –blocksize can avoid performance issues from tracking lots of 100KB blocks. Deduplication will be worse (does that matter?).