I've been running a large project with the Remove Overlap tool (mostly arcpy) and very frequently I receive the non-helpful Error #999999
It won't process large areas so I've been using a fishnet to select regions to process but some regions process and some don't
Changing the buffer size seems to vary which fishnet grids it fails on so it seems like it might just be a math/programming issue but I cannot see any particular thing that causes it.
Strangely, running the tool in Pro vs Python has different results, areas that won't process in Python will process in Pro and vice versa.
My current workaround is each time it fails on a fishnet grid, I created another smaller fishnet in that grid and that usually works but sometimes fails also (because these failures seem random)
It would be nice if someone could take a look at this tool and make it more robust
https://pro.arcgis.com/en/pro-app/latest/tool-reference/analysis/remove-overlap-multiple.htm