Aliases broken after restore
 

I used SD to copy all files internal->FireWire->internal (the same way a disaster restore would go) in an attempt at defragmentation. The volumes were named Macintosh->Clone->Macintosh. SD was allowed to erase target volumes.

After booting from the restored internal HD (FireWire disconnected) I noticed several issues with aliases. The affected applications are probably more at fault than SD, but I think a list of possible problems belongs in the documentation of a program claiming backup capabilities.

An entry in the Finder sidebar pointed to the wrong folder (and changed its name accordingly).

Retrospect subvolumes pointed to different folders.

Retrospect could not find its catalog files.

That curious, garoomph. Perhaps those applications are relying on File Numbers rather than on paths.

I'll make a note of that general issue -- though not specific applications -- in a future version of the User's Guide. But, as you said, it's more an issue with the application. If Retrospect can't find its catalog files after a restore, and had problems with subvolumes, it wouldn't work after a restore with itself, since it doesn't keep file numbers the same either! :)

Now that you mention it: I experienced that (full volume restore). It really doesn't...

It's just not possible to keep file numbers the same unless you're doing a low-level, sector-by-sector copy. Unfortunately, it's a basic limitation of all file-copying programs.