You will acquire more and more knowledge while you work.
You will acquire more and more knowledge while you are working.
What is the difference between them? Which sounds more natural?
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There's no significant difference in meaning between your two example sentences.
The conjunction "while" means that whatever follows is a continuous time that happens at the same time as the main clause, so regardless of whether you use a simple tense ("you work") or a continuous tense ("you're working"), the reader understands it means a continuous time and they're both natural.
One might feel somewhat more natural than the other in a specific context, but without that context, it's impossible to say which is more natural.