I had this happen to me as well with an AA flight I had flown that was credited, and then disappeared subsequently (happened about 1.5 weeks ago). Called into MPC hotline and they acknowledged it was a technical glitch they are working through (I also checked FT at that time but did not find anything, so figured it was something that only impacted partner flights or some other small-ish subset. Given the timing of OP's post though, it looks like I probably missed it since the subject of the thread seems to differ slightly with the issues people have been posting about subsequent).

In any event, they advised that I email them the e-ticket and boarding pass so that they could re-credit it manually rather than waiting for the IT team to resolve the technical issues (and then re-credit everyone), as they did not have an estimate of how long this would take. I only had my e-ticket, but they were still able to help me credit it back (I guess because it had already previously been credited?) within a couple of days after I emailed them.