I tried to overwrite a web layer using Pro. The process errored out and deleted the original web layer.
I was only trying to update the layer because online popups stopped displaying entirely - can't make them work in any way.
I'm quite sure someone will be round to tell me to contact Tech Support or tell them about it in the Pro forum. But this isn't a situation I can reproduce or explain how anyone at tech support should reproduce these problems. So they'll go unnoticed to the larger public unless I post about them here.
Allow us to commiserate (at least, it sounds similar)! We have a Pro Project for updating a seasonal map ... went to republish the layer, overwrite failed and now the layer is 'stuck' in Portal (we can't access the Settings .. the 'loading' icon is all we get).
We published a new layer and reconfigured the map to get us through; cleaning up the 'stuck' layer is pretty far down our list of priorities, but it is annoying!