I decided to get a larger SD card for my setup and do away with the connected HDD setup I had. Now I just have a 1TB SD in the MiSTer and no connected storage. Everything is fine and working good except one thing. So far on both the PS1 and Saturn cores I'm unable to change discs without rebooting the entire core. In the past I could boot up say Symphony of the Night, get bored, go into the menu and pick another game and it would load right up. Now it doesn't work that way. In the PS1 core it just flashes the currently selected region and the current game stays mounted. To change games I actually have to reboot the MiSTer and restart the PS1 and Saturn cores.
Using the update_all BIOS and game images are unzipped and .CHD files Same with Saturn. This same workflow worked fine with my previous setup.
Does this sound remotely familiar to anybody else?