It wasn't as if he didn't work just as hard as I did --- more so, probably.
It's just an example sentence I quoted from a dictionary. I know the definition of "more so" but does more so in this case means that he worked even harder than me?
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...does more so in this case means that he worked even harder than me?
Yes, but the word probably is important here. The speaker isn't certain that the other person works harder. The speaker is guessing about that. However, the speaker is certain that at least they worked equally hard.
This kind of sentence might be used when another coworker received a promotion and you didn't.
"I thought I deserved the promotion more than him. It wasn't as if he didn't work just as hard as I did --- more so, probably. However, many customers complained about his rudeness and he was often late to work."
The probably in the end is modifying the more so. Meaning that the writer is only assuming that the person in the sentence is working more than her.