Will publishing a new EXE (x86) version replace an existing MSI (x64) version of the same app in Intune?
When you use “Publish New Version of Selected Applications”, then it will only publish the ones that are selected, in this case, it should only update the EXE and not the MSI. But it is important to remember, that we only update apps that were originally published via PatchPro, we cannot hijack other apps, which were created manually or by other parties.