I had to do some work away from the server that houses our GIS data. I created a Map Package so that I could take in on the road with me. Everything worked great away from the office. When I returned I open the .mpk and saved as an .mxd to the server and resourced all the layers to the appropriate geodatabase data on the server. Everything seemed fine, so I saved the .mxd and closed Arcmap. Unfortunately, the resourced data does not stay and I have to resource it every time that I open the .mxd. I even tried deleting the layer and adding the .lyr files again. this doesn't help.
- Repath your data using arcpy: http://desktop.arcgis.com/en/arcmap/10.3/analyze/arcpy-mapping/updatingandfixingdatasources.htm
- Open the mxd and another blank mxd. Copy the layout elements to the new mxd and drag the layers across and save as a new mxd (the original mxd may be corrupt)