I shoot PEFs, then use the Adobe DNG converter to create a DNG copy. I keep the PEFs as an archived copy on a separate hard disk. It sounds tedious but Lightroom can be set up to do all that automatically, it just takes longer. The advantages:
- PEFs are harder to open and change so they make good archive files.
- The converter reads the files right from the card and flags corrupt files immediately. You know about a problem in time to fix it.
- The DNGs make great working files because changes are stored within the files, so there are no sidecar files to lose.
- It's automatic.
Disadvantages:
- Doubles import time at least.
- Lightroom changes are not archived by this, so your import presets and edits would have to be redone.
I don't know how that applies to Aperture but the system works for me.