Kajsa, that does not solve the problem I've been having.
I have tried using the tool on dendritic terrain (sinks filled) and I got a total of 20 watersheds delineated out of thousands of polygons. ALL of the BatchDone fields are converted to -1 afterwards, even the ones that worked. The message at the end of the process says "0 polygons processed out of 11789". If the issue was the BatchDone field being set to 1 or -1, then the message would say that certain polygons were skipped or that no polygons have BatchDone = 0.
Here is my alternative to the "Batch Watershed Delineation for Polygons" tool:
Sink Prescreening, Fill Sinks (all sinks even real ones), Flow Direction, Flow Accumulation, convert polygons to raster, Catchment Grid Delineation (using the rasterized polygons as Link Grid), Catchment Polygon Processing etc...