I am running ArcGIS 10.3 ArcScan and trying to clean up a raster prior to vectorisation. The raster was a three band raster converted to greyscale using the 'Greyscale function', classified into 2 bands using the Symbology tool and saved as a new raster tiff in a folder (for this method see How can I flatten a multi-band raster to a single-band raster in ArcMap 10.2?). I can vectorise the raster using ArcScan, but I need to clean it up first using Raster Clean and the Raster Painting tools. When I try to clean it up the eraser appears to work, but when I let go of the mouse button all the erased pixels reappear. Nothing I can do seems to help. I have tried moving the tiff into the same folder as the shapefiles I am editing and will use for vectorisation. I have also tried exporting the tiff and shapefiles to a gdb. I don't know if this is because this was a greyscale raster that is then classified into 2 bands for vectorisation, or if there is some crucial step I am missing that would allow me to clean up my raster in ArcScan.
Experienced the same issue in 10.4.1 and suspect that the reason lies with the fact that my raster had been georeferenced to a coordinate system (transverse mercator) with a shift in central meridian. I believe that the shift or the funky coordinate system extents is causing the edits with the raster to not "see" the the actual pixels. An inelegant fix I used was to project the raster to the same coordinate system and use that reprojected raster for vectorization.
I've now done some experimentation with vectorisation and raster cleanup in ArcGIS 10.4. I've discovered that it will work with a transverse mercator projection (mine is WGS 1984 UTM zone 36N) but you have to have the Data Frame, the raster you want to vectorise and the shapefile you're going to be vectorising to all on the same projection.