All are generally acceptable for a response. I find that my response changes based on how well I know the person or not.
If I am fairly familiar with them (close friend or good friend) I may say:
Hey no worries!
used in rare occasions that you want to acknowledge and show you are happy that your words meant a lot to them:
If someone says it that I am not so familiar I tend to respond:
English is weird where there are many ways to say the same thing. Many responses are appropriate for the same thing. I would just say what you feel is a natural response.
I prefer "no worries", others may say "no problem". Pretty much the same meaning or implied meaning using a different word.
In the above example you provided, their response of "that means a lot" can be interpreted as saying:
Hey, I am glad you acknowledged my hard work and dedication to improving so it means a lot, thanks!
So I would word your response as if you are responding to that :) In the end as I said, there are many ways to respond and all the above are equally appropriate. Find one that feels natural to you and go with it!