To answer your question simply, only the first variant of that sentence is correct. That being said, very many people will use the second, and since English is an ever-changing language there will probably come a point in the future, possibly a very close one where it will be considered correct. The reason only the first is correct is verb tense consistency. In other words, if a sentence starts in past simple, it stays in past simple; if it starts in present perfect, it stays in present perfect.
If you say, "I tested the program with this input data..." then your sentence is in past simple, and so the rest of the sentence should be as well. Therefore, "... and it does work." is the wrong tense. The correct ending to the sentence as started above would be, "... and it worked." The entire sentence is therefore in past simple.
Having said that, It's worth reiterating that it probably will be used like this about as much as it isn't. Naturalness does tend to win out over correctness, and then becomes correctness for as long as it takes for something else to feel natural.