Acknowledge somebody whose advice is not relevant to the current manuscript anymore? I received some advice from two researchers, which were helpful at the time. So, I mentioned the researchers in the acknowledgements section of my paper’s early version.

After the first draft, the paper has been substantially modified, and their advice is no longer that visible on the paper. Should I still keep the acknowledgement? I feel it is difficult to remove it, since the paper is being circulated between more than ten co-authors. I would have to give some reason, but then I don’t know if I look silly for saying that their advice was after all not so useful.

What to do?
How to decide who to include in the acknowledgements?


Generously.
If people gave up their valuable time to help you in the process of developing that paper, it is kind to acknowledge that.  This is true even with contributions that are very helpful but may not be directly reflected in the final text, such as avoiding a long rabbit-hole or programming for some data collection or analysis part of it.
Per Mad Jack's answer, you can have the acknowledgement accurately reflect that the contribution was to an earlier draft, or whatever the contribution was, but they still helped.