Machine the nut or use a thin shim washer to achieve the same result, All you need is a new section of the nut aligned with the slot to re-stake. Loctite is a go, a new nut would be ideal but not necessary.
I would not restake the nut where it was originally staked in case the metal fatigues and chips off in service leaving a chip of metal on the loose in your cases.
A pin drift to tap the collapsed section of nut out of the groove as best you can achieve and then back the nut off, as has been said, the nut is softer than the hardened gearshaft and will not mar the threads.