This is in the spoilers section so I am not going to spoiler tag the dreaded B word in this post. It's ridiculous.

So I collected about 17 crimson ninroots in Blackreach for 'Return to your roots' however I used them to make invisibility potions. Do I have to collect 13 ninroots or another 30?

all 30 again

Unfortunately, I did the same ha.

But my quest didn't update the loss of the nirnroot, so it was still at the 18 I had before I used them up. Then the next one I picked up moved the count to 19.

May have been a bug though.

Yes you have to collect them all over again, so you have 30 in you inventory

Using one should reduce the count by one, etc. So, likely the OP should collect all 30 again. This is not a necessary quest to do, though.

It gives a real nice reward though, definitely recommended for alchemists

Just run along the north shore at night. You'll see 30 within a few minutes. Easy-peasy.

Wrong nirnroots. He needs the crimson ones from Blackreach; regular ones from the surface don't count.

I used up all 18 of my c-roots, the count stayed at 18 and the next one I picked up moved it to 19.

This for sure.

I know the game claims Nirnroots don't grow back, but I think they do because after I gathered 30 (over several trips to Blackreach) there were still some in the ground - even along normal pathways that I know I had already picked.

Also, you can store them somewhere so you aren't always carrying them as long as you give 30 to the recipient.