The details of your situation are a bit unclear to me, but what you are seeing appears to be a CADimage data file that thinks is open for read/write operations (perhaps it is, or perhaps it just hasn't been properly closed).
I don't bother with making container files since I don't find the speed difference to be significant. When I use the GS supplied and 3rd party libraries I leave them as intact containers just to ensure that they remain unchanged, but office standard and custom project libraries I just keep as loose parts.
If what you are trying to do is combine all your libraries into a single container I recommend against this. It will take more time and cause more trouble than the small speed improvements are worth.