MXD changes no longer prompt warnings

Since I upgraded from GE 3.11 to 3.14 and GVS 1.7 to 1.9, I no longer get prompted for warnings when there are MXD changes.  Usually, if I add a new layer in the MXD, or change layer order, ungroup layers, add groups, etc, the next time I edit the site in GE Manager it will throw a warning that says the layer is missing/new/not in the group/etc.  Failing that, at least there is the warning icon at the top, to the left of “Configure Site: SiteName” that I can click on to see and fix the warnings.  But now nothing happens.  It never shows any warnings, the icon is not there, and my new/changed layers don’t show up at all.  I have to manually edit the site.xml to add the new layers or make the changes.  I run into problems with layer IDs, since they all change in the MXD but not in the site.xml.  I have to be really careful to add layers with nothing other than a layer name, otherwise when I edit the site in GE Manager it gives errors in red text (something along the lines of the layer ids being messed up, I can’t remember exactly) and basically disables the whole site and won’t let me edit it at all in manager.

If I can avoid the layer id problems and successfully add the new layers to the site.xml and reload the site, then when I edit the site in GE Manager it will give the warnings and then properly set up the new/changed layers and reassign the correct layer IDs.  Business as usual.

Fortunately I only added two new layers towards the bottom of my MXD so it was relatively easy to add them in the site.xml, but I can see huge problems will occur if I make a lot of changes.