ArcGIS Desktop (and its upgrades) should in no way affect your ArcGIS Online web apps, as these are two completely separate applications. Are your pop-ups working in your web map?
EDIT: If your services are hosted on ArcGIS Server and you upgraded this, this may have caused the error.
Yes. Just can't configure. I go the layer of interest, more option, hit configure pop ups and it will not produce the configure menu. I been doing this for several months. Not sure what the problem is.
We just upgraded to 10.4.1. Also updated some parcel data.
Hosting the services on ArcGIS Server.
I do have a couple of layers or datasets that allows me to configure popups. But I have a few datasets being used never updated that will not allow me to configure. I did try to create new maps to see if there's something wrong with the current files I need to configure. I found nothing in common.