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I guess the easiest solution might be as you suggest and rebuild the standby databases from scratch after the non-CDB to PDB conversion. However, if for some reason that is not an option, you can convert to PDB without having to re-transfer the data files.
The data guard PM posted this blog a while ago:
And this MOS note can help as well:
2273304.1: Reusing the Source Standby Database Files When Plugging a non-CDB as a PDB into the Primary Database of a Data Guard Configuration