Just installed Boinc again and set up seti and milky way from old accounts, then I remembered I had a bam account so told the client to sync with that, once it synced it removed both projects from my project list and now I am left with nothing.
Any ideas?

Yes, you have to attach to the projects through BAM! Otherwise, they'll be detached again by BAM! as you have experienced

Try the Sign-up for projects link from My BAM menu to the left of this page and use the "Find account" radio buttons.

Gruß,
Gundolf
[edit]If you can't find "your" projects on that link, check your Host list[/edit]

They are attached through BAM and always have been.

So, you first attached using BOINC manager, and then (re)connected to BAM!

If you say

check the "Attach?" field in your host details (reachable through your host list).

Gruß,
Gundolf