Here is the scenario. Defendant pleas to 3rd degree (we thought). Judicial confession alleges SJF. Defendant sentenced to 3rd degree punishment. Appeals. Appellate attorney files Anders brief. COA looks at record and discovers above error. Returns to Trial Court. Now I have a letter stating appeal reinstated.

Who has jurisdiction?

It is on appeal so jurisdiction lies in the COA except to the extent it has sent the case back. In other words, the TC can do only what the COA allows it to do. Because there appears to be a conflict between the COA's orders remanding and reinstating, you might want to seek clarification from the COA.

Presumably the initial action of the CoA was solely to provide the trial judge with the opportunity to appoint new appellate counsel (to brief the "arguably" meritorious issue discovered by them). If that has occurred, then the court will again have to examine whether the error was in fact reversible. See Guerrero, 64 S.W.3d at 442.