Oh... that should only happen if you were mousing over an entity and saved. Nothing I can do about that. There is a shortcut and key-combo (ctrl-m by default) to disable to map hiding.
I could add a command to enable the minimap for a player, that only works for admins. Would that help you in your current game? (if running a command would disable achievements).
If running a command is ok:
/c game.player.minimap_enabled = true
There is no situation where that is possible except where a mod has disabled "update_selected_entity". The selected event will always fire unless there is a bug in Factorio itself. My mod strictly listens to that. Can you share your modlist?