When the rename tool is used it only renames the feature class and keeps the old name as an alias. This causes confusion when the renamed feature class is brought into Pro the OLD name shows the TOC. There should be at least an option in the rename tool to also rename the alias. The only way to do this currently over a group of layers is to run a separate script (arcpy.AlterAliasName).
This was addressed in ArcGIS Pro 3.0 in a different way than providing an explicit option. Rather, the Rename tool now ensures that the new alias name is the same as the renamed feature class. This should help alleviate the confusion caused by keeping the former alias name.
See Ideas in ArcGIS Pro 3.0 to see this and all of the other ideas you can look forward to when you upgrade.
Also be sure to check out the What's New documentation: https://pro.arcgis.com/en/pro-app/latest/get-started/whats-new-in-arcgis-pro.htm
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