Stumbled across this thread just now. Weren't these leased directly from EMD?
The late 1980's was the period when EMD were getting into the short-term leasing and resell business themselves, so it's possible that Conrail wanted to buy them, but EMD simply refused. Not every 15 year locomotive lease has a purchase clause that the road can exercise.
If I'm not mistaken, didn't this scenario also happen with 100 Conrail GP38-2's coming off their 15 year lease right around this time? EMD never even gave them the opportunity to purchase them even though CR wanted to, since EMD had more lucrative plans in mind for them.
I think there was a group of CR GP40's, recently overhauled, that went similarly a few years before this (Including the units that ended up on the Rio Grande). Not sure if it was EMD that time, but this was another instance of good 2nd generation power going before its time, despite CR wanting to buy them. The lessor had more lucrative plans in mind for them and reclaimed them without giving CR the chance to buy them.
I bet that Conrail would've loved to have kept these, but either didn't have the opportunity or couldn't justify the purchase price.