This is the expected behaviour from Denodo Platform. Whenever Source refresh is done, the wrapper will be updated with the underlying data source configuration.
For your case, I would re-create or alter the wrapper output schema with NULL VALUE inline constraint property by executing the below command from the VQL shell:
ALTER WRAPPER DF <name:identifier>
field1 = 'field1' (OPT) NULLVALUE '',
field2 = 'field2' (OPT)
For more information, you could refer to section, [DF Wrappers](https://community.denodo.com/docs/html/browse/7.0/vdp/vql/generating_wrappers_and_data_sources/creating_wrappers/df_wrappers#df-wrappers) of Virtual DataPort VQL Guide
Hope this helps!