Not sure if I quite get the gist of your problem, but this might solve it:
call UnitMakeAbilityPermanent( <your unit>, true, <ability id> )
Replace the bits in <>. That will make an ability remain on the hero when he morphs.
Edit: Okay, I think I understand your problem fully now and no, there is no easy way. You can either trigger it completely, or trigger the morph so the original unit is hidden/paused for the duration.
@FhelZone, so, you want to change the transform ability without reset cooldown of the old ability ?
If so, I think you can use the Engineering Upgrade ability,this ability must upgrade from the Chemical Rage to Metamorphosis, (put it in a disabled spell book, of couse) then when you add that unique ability to a unit, add this too. This unit will get the Metamorphosis with current cooldown of the Chemical Rage
No, if you play my game, you should be able to purchase some spells. Transforming will remove the spell that you have purchased. Now my trigger that keeps it alive is every second it returns the skill. By the way Jazradel, is that trigger of yours right if yes well it should be the answer, Maybe. And the skills are stored in a variable, how should I use the skill ID.
Ghan has said he has fixed this. Monovertex please confirm this fix. This was only a problem with people that had signatures in the upper levels like not the special members but the respected members.