Maybe someone can help, I'm flying back to the UK on Thursday from YYZ but have to change in JFK and pick up a connecting flight.

The flight was booked with Delta but has a code share with Virgin. Flying Delta from YYZ-JFK and Virgin from JFK to LHR. I will be checking in online so I can pick my seat in advance but do I need to check in online for both parts? I have two confirmation codes, one for Delta and one for Virgin so am able to access the online check in for both..kind of puzzled. Any help would be appreciated!

I could be wrong but usually when you change airlines you require a separate check-in.
If both of your legs were AC for example then you only need to check-in once.

Also just to note that whenever I have checked in 'online' my seat selection has changed by the time I get to the airport.

OK thanks, I have done a two-parter before but always with the same airline so it was one check in. That's strange about your seat selection, never had an issue with that.

All depends on the airlines involved when it comes to code shares, some can check you in for the code share and some can't.

If you have 2 unique conf# for each airline, good chance you will need to check in for each on their own.

When you check in for the first one it should be obvious if you've been checked in for both as it will give you two boarding passes and two opportunities to select seats, etc.

It lets me pre-select a seat for my flight with Delta, but for the Virgin flight it linked me to Virgins website. Which makes me think it will be two separate check-ins

Yep, sounds like it.

Turns out I only had to check in once at Toronto. They were overbooked too so I volunteered to take a later flight (1 hour later) and got a $600 voucher for Delta, plus they kindly upgraded me to business class for the portion of the flight to the UK. Very, very nice flight with a lay flat bed!

Awesome! Glad it all worked out in the end!