Title pretty much sums up the entire subject matter.
We use to use HTML but are now using Markdown, is there an effective way to convert those old replies/threads into Markdown?
To fix the invalid-files issue see the discussion in this thread https://community.nodebb.org/topic/15075/nodebb-v1-15-0-rc-0-release-candidate-published/7.
Specifically you need to update the multiparty dependency.
You can ignore the second it is just a warning, that plugin will need a update to use the slugify module in the future.