I have the same problem with maven javaee web project NetBeans 11.3 not in NetBeans 11.2 but I am facing with this problem many years almost in all NetBeans version. I am still looking for solution but only when I change the red flagged Entity (add space and remove space and save and compile) than the red flag disappear. When I finish "doing nothing" with theese entity classes but triggering something in NetBeans all red flags disappear. If I do clean and build the status remains good. If I clear the NetBeans Cache the problem starts again.
– Miklos KrivanApr 18 '20 at 08:27
See my answer here: https://stackoverflow.com/questions/9847483/why-doesnt-netbeans-ide-see-the-generated-sources/61303952#61303952
– Miklos KrivanApr 19 '20 at 12:05