That's pretty much the exact situation I'm in: I bought what was called the Digital Edition in the mid-2000s and then got a separate license for Triton much later on; by then my licenses had been migrated to Korg ID as separate products.
Yesterday I have logged a support request to know what's my upgrade path, but unfortunately Korg does not seem to have a great track record at replying to those. The detail you have pointed out is the most surreal part of this affair: the LE plugins, which are usually free with the purchase of hardware controllers (and possibily magazines too?) DO have an upgrade path, while a legit owner of the full software is apparently supposed to pay full price. I really hope this is not the case because I'm in love with this round of updates.
Kindest regards,
--
Marco