Hi Andy,
When you do the update FeatureType, are you ensuring that you click through the details in Parameters > Table List to pick the featuretype that you want to read from to update your attributes from the correct place? Perhaps you are updating the attributes from the wrong table...
Having said all that it does not matter, even if the attribute is not visibe on the reader, it will still be read, just not accessible to workbench unless you a) Use an AttributeExposer or
Manually add it. You only need to add or expose it if you need to do something to it in your workspace. Assuming the writer is dynamic, it will get written. To manually add it to the Reader just go to Readers > Import Feature Types and pull in the one you want, just so you can inspect the name and data type. Now go to Tools > FME Options > Workbench and click the option to "Allow reader feature type editing". Ok that and now add your attribute manually to your dynamic FT. As I say, this is not necessary but can be helpful if you don't want to expose the attribute later.
Having said all of that just re-adding the FT again by adding another Reader will not cause you any trouble other than you'll need to make sure your writer is still hooked up to the reader once you delete the incorrect Reader.
Thanks, Dave