Jon,
I don't know about Workflow Manager, but this can be done via the Platform Service (if that is what you mean by "web service").
POST to the DocuWare resource:
/DocuWare/Platform/FileCabinets/{cabID}/Documents/{docID}/Fields
The post data (XML) looks like this to clear out all keywords for a field:
<?xml version="1.0" encoding="utf-8"?>
<?xml-stylesheet type="text/xsl" href="/DocuWare/Platform/Content/standard.xslt"?>
<DocumentIndexFields xmlns:s="http://dev.docuware.com/schema/public/services" xmlns="http://dev.docuware.com/schema/public/services/platform">
<Field FieldName="<field_name>">
<Keywords></Keywords>
</Field>
</DocumentIndexFields>
I just tested the non-.NET routine I wrote to do this and was able to add, modify, and clear out keywords no problem. I imagine in .NET you simply pass an empty keywords List (or "null"?) to whatever method wraps the SDK resource.
Hope this helps, if using the SDK is an option.
Thanks,
Joe Kaufman