The only way to deal with that rust is to completely remove the lights, the cover and all the silicone shit to get back to the bare metal. The rust then needs to be dealt with.

If the removal is done with care the tail light conversion might be able to be saved. But that's a very big MAYBE!
I suspect that it wasn't done properly in the first place, with shitty workmanship, they probably sealed rust in under filler.
Another possibility is that the filler used is too rigid to deal with the body flex causing it to crack and let water in which in turn causing rust, a more flexible filler would be required or sufficient reinforcement applied to the area to prevent the flexing, the problem with that is that you might just transfer the problem to the next weakest point.
Probably easier to go back to using standard lights.

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