Had similar experience recently.

Reservation outbound SFO-KIX-TPE; inbound TPE-SFO. SFO-KIX had confirmed PZ upgrade with PlusPoint. KIX-TPE was on EVA. TPE-SFO was United. Regular economy with W class on United segments.

I had to change departure date. However, on "flight change" page, I had difficulty to specify SFO-KIX to W class and KIX-TPE (BR) to B class. Decided to cancel entire ticket and rebook. Thought was faster.

Say the confirmation number was ABCXYZ with $2000. Here is what I got:
1. Got the email that I had $2000 of FFC from cancellation of ABCXYZ.
2. On My United Travel Credit section, $2000 FFC was not listed with other FFCs.
3. Was able to see this FFC by using "Search Trave Credits" feature. However, when I booked a new ticket, this ABCXYZ credit was listed among other FFCs but grayed out. ABCXYZ was a stand-alone and couldn't be combined with other FFCs.

My workaround was to chat with an agent to book a cheap $75 SFO-LAS one-way by using the ABCXYZ credit. Agent said I could use remaining $1925 for online booking. Later I cancelled SFO-LAS ticket. I got $1925 and $75 FFCs listed on "My United/Wallet/Travel Credit" section. After that I could book new ticket online with combined values of these two and other FFCs.

Not sure if the hassle was due to confirmed PlusPoint upgrade or EVA-operated segment as part of the itinerary?