We were also hitting this. Tracked it down to wildcard syncs not working reliably. Some settings in advanced settings may cause it to not use them in some circumstances, especially the Max Size Per Batch setting (the smaller you set it the better - entering 2048 will actually save it as a negative number and will work reliably), but there’s not an exposed setting to just disable them entirely. However, you can change this one line in WorkspaceUpdate.cs to false and it will never use this optimization.
leaf.CanUseWildcard = false;
This thread was helpful. Got me experimenting with settings which led me to this.