If you change the input file but not the feature types present as readers then this warning will appear. If you are confirm that this feature type contains data then you have to revisit and see why it is not reading else proceed.
Direct copy paste from the FME desktop Basic manual:
"Every time FME reads a dataset, it checks the feature types inside that dataset to ensure
that they are all defined within the workspace schema. If there are feature types that exist in
the dataset, but do not exist in the workspace, then features are classed as "unexpected"
and filtered out by a function called the Unexpected Input Remover.
The actions of the Unexpected Input Remover are reported in the Log file:
STATS |Router and Unexpected Input Remover(RoutingFactory): Tested 3995 input
feature(s), wrote 3995 output feature(s): 957 matched merge filters, 957 were routed to
output, 3038 could not be routed
...and also through a dialog that opens
Remember that there are two different types of file dataset: file-based and folder-based.
For file-based datasets, if there is a layer in the file that is not represented on the canvas
then FME treats the layer as "unexpected" and drops it from the translation.
This most commonly happens when the layers in the source data change, or a completely
different file is selected.
For folder-based datasets - where layers are stored as separate files in a folder - if there is
a selected file that is not represented on the canvas, then FME treats the file as unexpected
and drops it from the translation."
Hope you are reassured now...:)
I think for clarity I will use separate Readers. In fact, I've added the Zip Writer as a second output in another Workspace which does other stuff to the CSV files.
With *.csv I only end up with 1 Feature Type called CSV in the Reader (Merge Feature Type is NOT ticked).
I had also tried using the Path Reader and FileCopy Writer as a way of Zipping the CSV because I don't really want to be handling schemas, just Zipping the files. However I couldn't get that method to work.