Overwriting brush setting does not update thumbnail from scratchpad. Choosing option "overwrite brush"creates copy of overwrited preset after restat of Krita.
This is intended behavior in Krita 4.0+. Overwriting a brush preset's settings doesn't overwrite the thumbnail. We were getting too many complaints about people "erasing" their brush icon with a white and asking how to get it back. In 4.0+, you have to be more explicit now by using "save new brush preset". You can pick the scratchpad area for the thumbnail, or load an existing image to use for the thumbnail.