Painless experience for me.

Booked a Jan-25 flight for my wife in Business using miles on the evening before the last devaluation (Feb time).
Booked an economy flight for myself as my renewal year is in July and had already used a voucher. Had some issues with this flight as I booked with OTA and missed out my middle name which is on my M&S account. So had to change this via feedback to TK (48h response time).
Called the centre to do and upgrade was done within 30s after going through security.

What I dont know... and am asking here.
Im currently transistioning my FF status from TK to Aegean.
This TK booking now has my M&S number + upgrade. What happens if I put in my Aegean FF number at the time of checkin? Is my upgrade linked to my M&S somehow? Its not alot of miles since I booked the cheapest eco class... so if there is a risk, I wont change it.