That's really weird as there is no magic to that at all. It's simply a file selection dialog to help you select a file and then that path is saved. What path has been saved in the config file? (In the extensions directory, you can go there through the aseprite settings). Have you saved it somewhere that changes? Onedrive-y path? Something?
Not sure which config file you are referring to but at least gmlink_connections.json shows the correct path? I am not using a onedrive folder.It doesn't show the name of the slice that I was updating though.
I was able to get 1 sprite to be added but that was only after I exited Gamemaker and told it not to save changes. I tried updating that same sprite via GMLink and then the sprite image changed to the one below. I try to edit the sprite file via GameMaker and it said the file is not found.