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Remove conditional encoding in `Update` and fix documentation

Patrick Rice requested to merge fix-further-issue-with-repository-file into main

Closes #1509 (closed)

One instance of the automated base64 encoding remained in the Update method, which caused an issue if the text encoding that was introduced in 16.1.1 was used to migrate files from pre-16.0 to post-16.1.1 logic

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