Thanks all,
I think it's almost back to where it needs to be. It wasn't as simple as just S/R and it was the audio files that were causing issues. My colleague and I have used the same file naming conventions and so I think files were clashing. There were no error messages but it just never got beyond one particular file, and there was lots of text about files on his version not being found in my version. I don't really know why it didn't just overwrite my version with his at that point, except if it was the file name confusion, but I'm grateful it didn't as that's how I knew something was wrong! I had to delete all the audio files, then S/R so they disappeared from LexBox and then re-add them - there weren't so many that it was a huge problem - and then repeat the S/R.
I had already created a backup of my correct version before messing with anything, so that will be used as a reference database as Bart suggested because some other things have changed and tomorrow the plan is to delete both projects from my colleague's computer and he will re-download from LexBox. Hopefully that will be the end of it! There wasn't a lot of text analysed so probably not worth going down the FLEx tools route, the reference database will speed up the work needing to be done again.
Lizzie