If I were you, I'd try to book the EY codeshare for the SN flight.
This 100% can be checked through, and a boarding pass/bags tagged through at check-in.

Without an EY# you are at the mercy of the check-in agent.
Interline agreement exists obviously as they codeshare with EY but it means EY paying SN some money for helping you -- so you might be out of luck.

Your VA status won't mean anything for the SN sector unless on an EY#.
Your AC status is useful for the SN sector, but EY won't care about that.

I recently had a transfer in BRU on EY# codeshare to SN and it was seamless.

Have fun!