Thanks for your reply, Yossi.
I think I should clarify that it's not just the categories that are already pre-existing but also (most of) the products. They are currently offered both through the main website and the micro site. I only recently joined the company - as far as I know they did try to reword the product descriptions to avoid duplicate content issues, however, I will need to look into how much they actually differ.
We want to retire the micro site, however, for these specific search terms related to what we sell on the micro site, the micro site does tend to rank better. So I suppose we would want to keep the copy from the microsite if possible?
In terms of DA, our main website is slightly better than the microsite, but both are very low - 18 vs. 12. I was told they never did any active link building and I cannot find a lot of links apart from our own websites through tools like OSE.
I have created a list of all existing URLs using Screaming Frog but that is a good point about using a few other tools to verify that my list is as complete as possible.