Should I merge my chapters to make them longer?
Should I merge my 300 - 600 word chapters to let's say 2k word chapters?
I would of course link up the two chapters so they flow into one another seamlessly.
If not then what can I do?
I think these short chapters are scaring off many readers.
You should put a poll on your fiction and ask your readers.
People complaining about short chapters are effectively complaining that they have to click an extra few times. Potentially hurting your story by combining what were originally separate chapters isn't worth that, because it's not like people are going to not read a story because the chapters are short, as long as the story is good.
This is referring to chapters already posted though. If you have some on the pipeline that are 300-600 words, and people are complaining about the new content being sparse... Maybe post more often? Or expand the chapters slightly if you can find a place?
If the scenes aren't flowing naturally from chapter to chapter and they're so short, that's possibly a problem for readers as well. When I'm writing I think of chapter breaks as pauses for dramatic impact after a short "arc" (as tanemrin mentioned) rather than as fully separate pieces.