I think I found a solution or at least a work around for this problem.
I encountered the same issue while copying a 270GB Aperture library to an external LaCie disk. Error 36 kept appearing after 60 or so GB. Rebuilding and repairing the library database did not work. Checking and repairing permissions did not solve it either.
As an experiment I tried to export my photo's from aperture in the following way.
- From Aperture select: FILE -> EXPORT ->SMART ALBUM AS NEW LIBRARY
- Type a Library name in the top field
- Then check both the COPY and PREVIEW checkboxes and choose a location where to export to. Then click EXPORT LIBRARY
Aperture starts exporting the complete library to the new location. No errors occurred. I replicated the same method on another mac and that worked too.
The whole process takes no longer than copying with Finder.
I found that when comparing the original library on my internal drive with the new library that in the new library there where 7 images less. I figure that those where corrupt images causing the error 36 while copying with Finder and Aperture left them out automatically in this export proces.
The new Library now works normally.
Hope this helps