I had these Collections:
Books (399)
Books || 2K - 20K (3)
Books || 20K - 40K (4)
Books || 40K - 80K (35)
Books || 80K - 150K (191)
Books || 150K+ (83)
Books: Short Listed (19)
Books: Up Next (15)
Books: Maybe (20)
Books: Low Interest (24)
Books: Worth a ReRead (15)
FanFiction|| 0K - 2K (89)
FanFiction|| 2K - 20K (560)
FanFiction|| 20K - 40K (154)
FanFiction|| 40K - 80K (186)
FanFiction|| 80K - 150K (186)
FanFiction|| 150K+ (145)
FanFiction (1320) (Now deleted)
FanFiction: Short Listed (43)
FanFiction: Kudos <100 (46)
FanFiction: Kudos <300 (232)
FanFiction: Kudos <600 (268)
FanFiction: Kudos <1000 (204)
FanFiction: Kudos <1500 (178)
FanFiction: Kudos <2000 (95)
FanFiction: Kudos >2000 (262)
FanFiction: Fandom 1 (1305)
FanFiction: Fandom 2 (1)
FanFiction: Fandom 3 (14)
And with this structure, the sync process is currently working (it takes just half a minute to process everything).
Yesterday, I loaded around 100 new FF, and the sync got stuck.
I deleted on the device FanFiction and Fandom 1 (the biggest collections), and it started working again. Today, I recreated through Calibre the Fandom 1 Collection (but I disabled the generic Fanfiction one) and it kept working.
So, my assumption is that it's having 2 collections with over 1K and something books that caused the crash.
I'm half tempted to add again collections (but keeping a low number of books in each) to see when the sync crashes again