Whether or not you can rely on the first hefsek taharah to go to the mikveh Thursday night depends on the color of the brown discharge. While some authorities reject any brown discharge on a hefsek taharah, there can be room to permit it, especially after the fact. The size of a discharge makes no difference on a bedikah cloth.
What color brown was it and under what lighting (fluorescent, incandescent, or sunlight) did you see it?
In the future, you should not wipe the brown off of the hefsek taharah and you should bring it promptly to a Rabbi.
Please note questions that need a quick answer such as this one are best addressed to our hotline.