I don't have much experience with Enhanced portals, but from what I understand, each portal has two Identifiers; unique and network. The unique identifier is specific to that portal and no other portal can have that identifier, while the network identifier is used to link portals together by having them use the same network identifier. Each of these are provided by a different block which you place in the portal frame (unfortunately I don't know the names of the blocks off the top of my head).
From what I can gather, it sounds like you're correctly setting a unique identifier on your nether based portal, and then in an attempt to join the portals as a network are trying to use the same unique identifier on the portal at your base. To fix this issue, make sure you have each portal with a different unique identifier, but with the same network identifier (different to the unique identifier).