R Shimon Taub (The Laws of Tzedakah and Maaser, p. 149) writes that
One who benefits by giving tzedakah because he ends up paying less taxes is not obligated to give that profit to tzedakah. Therefore if one would have had to pay $10,000 in taxes had he not given tzedakah, but because of all the tzedakah he gave must pay only $7,000, he is not obliged to give in the profit of $3,000 to tzedakah.
As such one would have fulfilled one's obligation even if reimbursed in part.
Note it is best not to make vows (nedarim) to charity lest one forget to honor his commitment and violate a Torah prohibition. Saying bli neder after a pledge is an easy way to accomplish this (see R Avrohom Chaim Feuer's The tzedakah treasury, p. 220)