You did the right thing to remove the dead roots and potting into fresh bark.
The arial roots may be able to adapt to be under the media, but it is best to keep them on the dryer side while they adapt.
I have a phal which since last summer has just had two ex-arial roots under the medium and thats it. I'm not sure if I did the right thing but I acutally removed the plant from the medium twice a week for about three weeks, to allow the roots to fully dry, but kept it most most of the rest of the time. I did this to try and ensure the arial roots did not rot before they adapted.
It seemed to work, in that those two roots are still alive and now adapted to being in the medium, but the phal still only has the two roots many months later (but it's still alive, which is the good bit).
Many people on this forum advise KLN to promote root growth, but I've still been unable to get hold of it in the UK. There is a UK website called Orchid Accesories which lists it but their security certificate is out of date and I keep meaning to ring them but... well... I'm very very busy during work/office hours and get home every single day, see my 'chids and think "I've forgotten to ring again".
While it's difficult, I would personally remove the spikes with that little amount of roots left. I had to remove two on mine over the later summer months, because it seemed determined to spike rather than grow roots.
Phal root rot, what should I do now?
the leaves were floppy yesterday and I automatically thought 'oh god root rot' so today I took it out of its pot and omg what a mess all but one under medium root was squishy and hollow and they had little white spots on so off they came, I had a fungicide so after I had removed all the dead matter I dipped the roots left which was one under medium root and two aerial roots into fungicide in water and gently eased the aerial roots into the pot and repotted in fresh bark I fear that the aerial roots will not survive as they are not used to being in the medium if this is the case there is only one root which is viable, it has two spikes on one which the buds are just starting to open. I am guessing I need to remove the spikes so the plant can concentrate its energy on new root growth but I am reluctant to do this unless I am told yes it is neccesary. as the buds are just starting to open on one of the spikes. Have I done the right thing and if not any advice please and what should I do about these spikes, I read somewhere that feeding with seaweed fertiliser stimulates root growth, does anyone know if this is correct or not ? just about at the point of giving up but battle on the other is healthy so I've done something right with that one so far. My Thunia alba is growing well and my Maxillaria and Dendrobium haven't keeled over and died yet so I am hoping I can get over this set back and carry on. I also think when I got it and repotted I should have taken the suspect roots off then but I was hoping they would be ok. so what now? is thre any chance this guy will survive or have I killed my second Phal 
I think I will remove the spikes then, though I cant get them to open properly both the buds are wearing hoodies 
the top and side petals are not opening out though the lower ones have. It is dry now as I only soaked the bark for a couple of hours, last time I repotted I soaked for about 18 hours and I think it was too wet when I repotted hence causing this problem when the roots were already not in a good condition. I will try rescue him and see what happens at this point I have nothing to lose on him. I just so have to learn to leave them alone and quit watering them 
think I am too keen and they don't like to be pampered 
I will Look into that or maybe you can tell me how it does on yours, I usually use water that has been in a bottle on the radiator on my phals as I do for my seedlings for the garden but I Have been known to use cold water from the tap. I will try make sure it is luke warm for this particular little guy.
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