So it seems like this issue has not been fixed, we are now on version 2.4.3 of Pro and this all started with the 2.3.2 update. I have been hesitant for quite some time to overwrite layers from Pro to AGOL because I knew it would be too time consuming to fix each layer that "broke".
I decided based on the recent posts on this topic to try it again yesterday. The ArcGIS Online Assistant does work IF you know what to do. It took me some time to figure out where to find what the new REST endpoint is.
For those of you who are like me -
you need to go to the AGOL Assistant,
click “I want to” View an Item’s JSON,
Click on the layer/item and scroll down to the DATA section – about the 4th line shows the ID number,
THEN you would go back to the “I want to” section, choose: Update the URL’s of Services in a Web Map,
Pick which map you are updating, a list of layers appears to the right,
Scroll down to the old URL of the layer that has gone rogue, copy it, come back to the top and paste it in the “FIND”,
Also paste it in the "REPLACE", but at the end of the line replace the original rest services number with the new number you just discovered in the above step,
Voila, it should un-break the maps/layers!
An observation and I'm wondering if anyone else has noticed - it only seems to break the map if the original REST endpoint was a Zero. Seems like if I've already updated the layer at some point and it has a new number other than zero, then it works fine. Anyone else agree or disagree so we can maybe pin this down for ESRI??
Another observation (and warning), two of my maps were made with the templates that are available and the other was not. That one that was not made with a template will not - seemingly after today's ArcPro patch - warn me that there is something wrong with the layer when opening the map. There is No error message like before, instead it just blows it away out of the map and if you aren't aware of it - because there was no error message - and you make some changes and save the map, now the layer that used to be there, all configured, all that work, bye bye.
The two maps that were made with templates do still warn you that there is a problem so that you know you need to go fix it with the Assistant.
I'm pretty sure that we can all agree on one thing, it is a total time sucker to have to either fix these maps from scratch by re-adding the layer, it's custom symbology, it's custom popups, etc., or even to have to babysit every single overwrite to make sure that it either absolutely worked or the Assistant is needed. Some people need to do a lot of updates, others of us probably should but are avoiding it like the plague - ESRI, clearly there is an issue here.