This would make sense as the Workflow to switch lists under a field using the list does not make a ''permanent'' change -- only seen as temporarily during the use of the ''form''.
The FILTER button calls on the STATIC field properties (or what was set as ''default'') list associated with the field.

We also see this behavior when using QC-Synchronizer and trying to map to a field using a list.
The best thing to do is to use a ''default'' list that is a ''superset'' of all possible values seen across all lists you swap in to the list field via workflow. You may never actually use this list on teh form, but the filter or mapping will work now.

True that will work having the default list be a superset but end users will see the superset when they try and filter which could raise different questions such as why don't I see these options in the form but only in the filter. For now I have just asked the end users to type the value they want in the filter which works as well for me.
I have not used the sychronizer in a while but your right...if it will only let you select from the list (no write in values) they you would need to have the superset as the default list.

Thanks for the idea.