I’m working with an animated Switch LOP that toggles between different geometry objects, which generates time samples downstream in the USD stage.

My question is: should this be cached?

From what I understand, it’s generally considered good USD practice to cache all animation. However, when I use a File Cache LOP (tested with several configurations), the resulting cache seems to strip or omit the animation data entirely.

You can't cache a Switch LOP to USD, it has no representation in USD. So whatever is switching your LOP is causing the ROP to not write out the USD.

goldleaf
You can't cache a Switch LOP to USD, it has no representation in USD. So whatever is switching your LOP is causing the ROP to not write out the USD.

I assume the expectation is that exporting a sequence with animated switch into a single .usd (or caching) will behave exactly the same as if you run USD Stitch of individual frames, which have different switched stages

if it doesn't behave this way there needs to be some warning as that would not be intuitive

Please log a bug if/as you identify caching points (specific LOPs etc) which aren't behaving as-expected and doing so silently. The Cache LOP, for example, has a number of conditions it'll generate warnings for.