I currently use ArcGIS Desktop to publish Packaged Map Files (.pmf) which are read using ArcReader. My data is stored in a File Geodatabase. Recently, I switched to using ArcGIS Pro to edit my data, but I have continued to use Desktop to publish the .pmf's, since Pro does not publish pmf's. I had no issues until recently, when my data started glitching in my .pmf. A layer will display at first, but when you zoom in, it suddenly disappears. Or only some of the features in a layer appear. It seems to only affect certain layers.
It seemed to begin after I added a new Domain to my File Geodatabase, using ArcGIS Pro. I updated my definition queries and symbology in my Desktop map (since the new domain affected them) and republished the .pmf. But it's almost as though Pro created some sort of "lock" on the data. If I open Desktop and edit one of the layers, then save and republish my .pmf, then the Reader has no issues seeing the layer I edited. But if I edit that layer again in Pro and then publish a .pmf from Desktop, without making an edit in Desktop, the layer will glitch when the .pmf is opened.
I am currently using ArcGIS Desktop 10.7.1, ArcReader 10.5.1, and ArcGIS Pro 2.5