Hmm. Haven't tested this with anything moved, but it shouldn't crash. If you deleted just the dex files, then they should be recreated automatically.
Btw: I tested this on JFv1.43_Holiday after upgrading (without wiping) through all ADP versions starting with JF1.41. Certainly helped me and fixed it for good.
May I suggest you ask Disconnect on freenode #android? He told me about this.