I certainly hope your complain isn't that an emuMMC save isn't restoring into sysMMC,
because at the first place the occurrence of the crossing between 2 MMC states it just a pure coincidence.
If you restore the save into emuMMC, you should not expect the save to pop up in sysMMC.
The linking of your profiles is just a coincidence. It appears that your sysMMC and emuMMC profiles have now desynced.
It is unknown why sysMMC and emuMMC profiles desync, but I theorize it's due to the user's actions.
(Maybe you updated the FW of sysMMC, or maybe game update of sysMMC, or maybe a BCAT update/update wild area news etc.)
Presently, the only way to resync the emuMMC, is to create a new emuMMC based on the existing sysMMC.
In any case, this is not an issue on PKHeX. I can only guide you this much