Hi Matilda,
I don’t have a solution to your problem but just wanted to mention I’ve been experiencing a similar problem. My thought is that something has changed in such a way that the import process is treating the “#” sign in the header line like a comment in a script (ignoring it). I’ve tried adding a “#q2:types” line below the initial column header line and find that this line is also lost following import.
You might try changing your metadata file to have a different initial header that does not have a “#” sign in it (“sampleid”, for instance). Here’s a link to other acceptable headers that don’t require a pound sign - Metadata Options
Maybe that will help fix your issue!
Todd