Did you do a cash upgrade fee (most likely) if done on the web (|especially if done while looking at seatmap)? Did you talk to an agent or use change flight and make an upfare? The later may not be easy for an agency ticket.

A problem with the first (most common) is you may lose the upgrade fee if you cancel (as it is non-refundable).
Additionally not sure if going the cash upgrade fee requires UA taking control of the ticket, but yes this ticket may be in a limbo state. You may need to ask UA to formally take over the ticket (with a small fee) but some corporate agencies have told UA not to do this. You may have escalate with your TA. It probably would have been best to check with your TA first as some do not allow / support what you did.

see Unable to change corporate / third party issued reservations via UA.com
and
UA taking "ownership" / "control" of a reservation made by a TA for a ($50) fee?
See "recent" posts on cash upgrades/

It is not uncommon for two separate tickets to be cheaper than a single ticket, but two separate tickets expose you to increased risks of schedule changes / irrops / ... you would need to personal track and handle issues that would not as big of an issue . Your TA may not encourage this either.