I published a service to Portal and am able to overwrite it. There are not issues with the project itself or the map when viewed in the map viewer.
However, when I create an app and share the link out after a few weeks suddenly some data won't be visible in the app anymore. The data isn't set to load at the default extent. You have to zoom in and check the layer on to view the data. I tried talking with our administrator about if there is an error or setting in server manager that should be checked or changed but they suggested I check the project or filter settings.
Has anyone else run into this? Last time I had this happen my only solution was to republish all the data & send out a new URL for the app and I'd like to avoid doing that same scenario every few months.
I'd say please contact Esri Support and have an analyst take a look at this. It appears there are a lot pieces in this puzzle and won't give you much of advice w/o looking at this.
Sorry couldn't help much