Currently (2019.1) you aren't able to upgrade the tranformer via the Navigator pane if the transformer is inside a closed bookmark. You first have to expand the book mark first before upgrading it. It would be nice to not have to expand each bookmark to expose the transformers before upgrading.
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+18- Safer
We're planning to look more closely at the upgrade workflow in FME 2020. Thanks for this additional input.
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