In AGP 2.6.3, I tried to copy a FC from one GDB to a FDS in a different GDB. The tool appears to process the FC and shows the status bar running in the Catalog pane. But the FC didn't copy. I refreshed, but still no FC. I thought the spatial references were the same.
After trying a few times, closing and reopening AGP, I went back to old reliable ArcMap and viola - the error message appeared "Spatial References do not match." It would be helpful to have this message also appear immediately in AGP rather than showing a status bar that gives the impression the copy process is working. That would give users the hint to use 'Import' instead, provided the GCSs are the same. If the GCS is different, when attempting to import a FC, it would be nice for the FDS to offer a transform option.
