Issue: Once the form fields are merged with data and saved, the resulting PDF looses all form fields tags. Upon using JAWS to read the saved PDF, the form fields data are skipped and not readable by the tool.

Question: Is there a fix to retain the tagged form fields?

Answer: Note that in the Output.pdf  the form fields are "Flattened". 

When flattening, the form field information is lost and the field value becomes part of the base PDF. It does not have any structure information and thus the there is no data for screen reader to find.

Instead of flattening, make the fields read-only. This way the fields remain intact for accessibility but cannot be modified.

The corresponding Toolkit method is:
SetFormFieldData("fieldname", "fielddata", Flag) 
Value  Flag = 0 sets the field to Read-Only

Value  Flag = -997 sets the field to Flatten

Full Toolkit sample code available

FormFill example.