A lot of orchids like to somewhat dry out between watering and/or can easily develop root rot when submerged in water. Looks like you've got root rot.
Acc. to my mum (she loves orchids) phalaenopsis orchids roots need to dry a bit before you water them again, so they really don't like this sort of "always wet" system like semi-hydro. That's why the bottom roots in your picture are all rotten, but the top ones (that likely get drier) are thriving.
She also said those rotten roots must be clipped out, otherwise the bacteria spread to the healthy ones.
Her suggestion is to simply use the traditional method, with an organic substratum: a mix of pine bark and charcoal, with just a wee bit of sphagnum (so you don't need to water them constantly; but do wait until it's dry to water them again). With LECA only at the bottom of the pot, for drainage.
Houseplants
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