Long story short, I reprojected my data into WGS 84 without realizing they would be exported into the same master source gdb, deleted the duplicates, but now see ghost duplicates of feature datasets and feature classes of what I deleted when first opening ArcGIS Pro.
Refreshing the geodatabase removes said ghosts, however, I am afraid that this problem will carry over to my data backup dataset and online data were I to update them.
Since then I deleted the duplicate feature dataset for all duplicates; however I still see the 'ghost' of the feature datasets below the real one. This seems to be an intermittent issue and goes away when I refresh my geodatabase.
I want to update my online data and backup data with this layer as it is the main layer, yet I do not want to export this problem to all my data. I have no way of going backwards with my Master gdb which is experiencing these ghost feature data sets and layers.
I have exported the master gdb into a folder to see if the problem is duplicated, yet I did not see any issue. I deleted the original gdb and copied the test gdb to replace, but I am still getting this issue today.
Images from today 10:45 PT
Ghost feature dataset duplicates
Ghost duplicate feature classes
Post geodatabase refresh