I'm not sure you can combine them, apart from picking the assy you want to keeop and using this in all of the parent assemblies. Then delete the other unwanted versions/locations of parts/assemblies.
To stop this function happening in the future you may want to turn on Unique Filenames.
Or you can open the parent assy/s and do a Replace Component. As long as the target component has the same 'mate planes/surfaces/etc..' then this should work okay. After replacing all in each of the parent assy's then delete the unwanted/un-used versions from the folders.
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