Permissions and problems with second SSD drive

I have a second SSD in my MBP replacing the optical drive. Have had no problems with it until the aperture library that sits on it started having issues. I've narrowed it down to a corrupt file in the database of aperture. I've tried running disc repair etc,. on it and it reports it's okay but now i have a bigger issue. I cannot delete, rename or alter any files on the whole SSD. I cannot tell whether this was a result of me trying to fix it but now i cannot even get aperture to attempt to repair or open because of permissions.

If i get info on this second volume i can check and uncheck the 'Ignore Ownership', i can chmod on the files so it appears there are full permissions but no. Instead if i try to do anything with a file it complains with a -50 error which i cannot reference.

I've run some SSD utilities over it but the SSD itself is not reporting errors.

So i'm totally stumped. What can i do to experiment further? I can (and have) copied everything across apart from the files that consitute the aperture database, so if i reformat then i will loose the database (but not the masters at least)

But i would like to be able to fix it in situ...

many thanks

Paul