Once we place via using the fanout in the BGA package. then we are not able to delete the vias which we have placed, we need to close the pcb file and reopen the pcb file then we are able to delete the vias.
Of course you use a plugin as kicad v6.0.4 doesn’t contains a native builtin bga-fanout-tool. Also your picture in your corresponding gitlab-issue (Not able to delete vias in fanout BGA package (#11262) · Issues · KiCad / KiCad Source Code / kicad · GitLab) shows clearly a plugin-icon (all icons on the right side of the phyton-console-icon are plugins).
As the kicad-core-developers are not responsible for the phyton-plugins you have to look for the plugin-authors and try to contact them.
Maybe there are also other bga-fanout plugins available?
After all you have a workaround: saving/closing/reopening. Not nice, but sounds not that hard.