Yes, you can transfer the holdings, under different folios, through single Transfer-in request form

For example, if you have holdings in two folios, 123456 & 987654, with 'XYZ' Mutual Fund. Please list the folio nos. in the Transfer-In request form for 'XYZ' Mutual Fund, and folios 123456 and 987654 with 'XYZ' Mutual Fund will be transferred to your AxisDirect account in a single request.