Thanks,

I have no idea, to be honest, I thought using accountancy software was supposed to make things easier, not make me have to manually check all the transactions to see where they have ended up...

I've gone back and deleted all the transactions pulled in automatically and removed the link, I'll update by uploading spreadsheets in the future so I know everything is pulled in correctly. Not ideal but at least I'm not confused and risking having my accounts all messed up!