If you use an Inspector within your FME workspace it will show you the data as it is in FME at that point in the process. This may not be the same as the data that's eventually written to output, even if you connect the Inspector to the last port before the writer feature type because the output format may introduce limitations, or have a different schema, or may be limited in what types of geometry are selected.

You can disable the Inspector(s) and tick the option Writers -> Redirect to FME Data Inspector. That will send all your output data to the Data Inspector rather than your output file(s) but that still won't give you 100% the same output.

Now, as for your actual problem, it's hard to say something meaningful about that without seeing your workspace and/or data. Can you post that here?

You're round-tripping from CityGML back to CityGML, right? Does it work when you process the whole file (i.e. leave out the AttributeFilter)? I know very little about CityGML, but I do know that there are relationships between parts of the data, and if you filter out one component it's possible that related items are affected.

Thanks for reply! It makes sense more and more.

I just used to workspace generator which did the trick for CityGML dataset! Thanks!

Thanks. Yes, Im going from CityGML to CityGML. Workspace generator hooks up the right 'settings' for reader and writer. When it comes to AttributeFilter - it takes a filter for each feature class then for it a proper filter. Cannot take just one.