Hybrid converted video loses 5 seconds compared to original..?

[Selur]

What's your opinion on converting the Hybrid-processed 59.94fps deinterlaced footage back to 29.97fps?

Assuming your content was real interlaced (not telecined, field shifted or similar; do not trust the flags of the source!) and you got real motion between fields, it depends on the content. If you have lots of motion, you can potentially lose 50% of the motion information, which can be visible.
Then I would not go or 29.97fps and loose that information. If the goal to create something for archiving (= keep as much quality as possible) I would not go for 29.97fps. For normal content, you just want to watch that isn't sports you can get away with throwing out that information.

Is there a method you recommend to convert the 59.97 video down to 29.97, or 24,

sRestore or RIFE.

Or will a down convert lose some detail and give poor results, especially where there are scenes where significant motion occurs?

Yes, throwing out frames can hurt a lot depending on the content and how it's watched.

(I do have Apple Motion/FCPX, and I might investigate FFmpeg minterpolate, which I just learned about.

minterpolate = personally I would even prefer mvtoolsFPS over it.
Motion from FCPX: no clue never used it

Cu Selur