The freeze drying process will not affect the resistant starch content.
The freeze drying and milling method is regularly uses for analysing samples.
See the attached scientific publication on the measurement of available carbohydrates, digestible and resistant starch in food. Page 3 of the publication provides a description of how the samples are processed.
The publication discusses the use of the K-RAPRS method for the measurement of Resistant Starch in food ingredients and products.