Using AI 18.9.1 and updating a package. The UI detects the new version from the primary app, but the internal AppXManifest file did not get the updated version. In this case, only the 4th field of the version had changed in the app (causing an unnecessary popup in the detection logic that is only related to MSI builds), however I routinely run test builds with only the 4th field changing and have not had this happen in the past.
I upgraded to 19.0 and the behavior remained.
Looking into the aip file, I see that while the PRODUCTVERSION field was updated, there is a property later on IDENTITY that was not updated.
The <COMPONENT cid="caphyon.advinst.msicomp.MsiPropsComponent"> has a sub-element:
<ROW Property="ProductVersion" Value="1.9.2.14" Type="32" TargetFile="XXX.exe"/>
and later the <COMPONENT cid="caphyon.advinst.msicomp.FragmentComponent"> has a sub-element:
<ROW XmlAttribute="Version" XmlElement="Identity" Name="Version" Flags="0" Order="0" Value="1.9.2.3"/>
Manually editing the aip file field for that Identity attribute solved the problem for now, but AI needs a fix for this.