Changing an experiment due to preliminary data
Consider this:
What question is your paper trying to answer?

This is the real question to consider. If I were writing a paper about average milk production of cows and my question was "How much milk does the average cow produce in a year?" and then I only selected the 10 best cows, then I am really answering the question "How much milk do the 10 best cows in my selection produce in a year?".

If your paper's aim is to compare two or three algorithms, then there's no problem. If you write a paper about A and B, it's no different from writing a paper about A and C or A, B, and C. How you arrived at the algorithms does not change question you are answering.