Yep, they will respawn as
@reggikko said but what an annoying bug! I had to race around trying to harvest everything I needed before the NPC's 'weeded' all the plants out as I didn't want to have to hang around for them to respawn! Luckily I harvested everything in the Hermits area before he got around to 'weeding'.
Usually the plants will respawn the next day. I guess we should probably report this as a bug, tbh I completely forgot to when I saw this over a month ago. Oops!