Project Packaging in Pro blocked by errors over nonexistent layers

[JohnBranum]

Attempting to Package my Project in ArcGIS Pro 2.9, i'm blocked by a long list of "High" errors claiming that the sources for Layers i've deleted are inaccessible (error #00003).  Esri advises, "Hover over the analyzer message. Click the Options button that appears and click Remove Items With Errors", but "Remove Items With Errors" is not offered.  What is offered is "Select Layer In The Contents Pane" which proceeds to reload the item that was long ago deleted.

Months after deleting these layers, the Project has been saved, closed, and reopened; the cache has been cleared (Project > Options > Display > Clear cache - checked, project resaved, closed, and reopened), and i have excluded Toolboxes and History Items, and i've unchecked "Share outside of organization".  There are no other Jobs, and the package has no Attachments.

Any help...?

[MichaelVolz]

Have you tried to perform a Save As Copy in Pro to clean up the project?

I used this technique in ArcMap to remove ghost layers that were no longer in ArcMap as they had been deleted but there was still a reference to the data source buried in the mxd.

[JohnBranum]

So are you saying that just by Saving As it might just drop all the ghosts, or did you have to do something after that?

[MichaelVolz]

This is based on my experiences in ArcMap with a similar type issue when publishing services.  I have not yet encountered this issue in Pro.

I would record the mxd file size of the orginal file and the copied file and many times this operation drastically reduced the size of the mxd which was holding onto unused items.  This would be a check you could do in comparing file sizes of the aprx files.

[JohnBranum]

Well thank you, Michael.  I seem to remember doing that in Map as well, but sadly, it looks like a no-go in Pro.  Oddly enough, the Saved As was slightly smaller than the original too.

[MichaelVolz]

What type of data sources were used for the layers that were deleted from the Pro project?  Do these layers share a common trait.

[JohnBranum]

Apart from being simple point/line/polygon layers, the only thing common in this list is that all the layers were in maps and layouts that got completely deleted.  In fact, many of the layers listed have been pulled back into the current map and layout, and they work just fine there.