I got an email and was told something "Not positive but pretty sure" about something.
What does it mean? Should I expect a negative/bad news or I should assume that it will be a certain thing?
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No, the positive here is not in reference to how good or bad the news is. "Positive", in this context, means "certain".
So what this means is that they believe something is likely but are not 100% certain.
"When was Pluto downgraded to a dwarf planet?"
"I'm not positive but I'm pretty sure it was in 2006."
You would be justified to hope for the best.
So your sender has no certain proof yet, but expects the outcome to be as expected/discussed.