According to the standard MS document, It is not allowed for Lithuanian country region to generate the Intrastat report, when Lithuanian country has been selected as added country/region as part of Multiple VAT registrations functionality.

Customer statement-

Lithuanian is not a small country; it operates on huge number of transactions. Along with that customer has configured the Multiple VAT registration setup in their environment and now they are struggling to generate this reporting's.

Requesting the Product group team to help customer, by considering this country/region as per of Multiple VAT registration configuration.