You could do multiple transactions of lower size back to yourself until you get fewer inputs, and with them, make the last transaction.

Example:

What you are doing:
- Transaction 1: 20 inputs -> 1 output (A);

What you should do:
- Transaction 1: 10 inputs -> 1 output (A);
- Transaction 2: 10 inputs -> 1 output (B);
- Transaction 3: 2 inputs (output A + output B) -> 1 output (final destination);