I have a netherite sword and pickaxe, both enchanted with a couple books. The orb xp level on them are low (sword isn't that much). I went to go fishing as they regain the xp that way, but in doing so it doesn't seem to work.

No messages show and some of the orbs stay out at sea. They probably get confused with the fishing line. Although I have found that mining with my axe in hand does level up the item, if collecting ores. In fishing however I don't switch to these netherite tools & weapons because it'll be too late as the orbs are so fast. I don't think I can put these tools into any blocks to up the level with the orbs I collect myself directly. It seems to just affect stuff in my hotbar. I'm not sure about the rest of my inventory, but my elytra I wear isn't affected at all and that's enchanted too.

Usually all of the orbs would come my way like a magnet. There's something stopping that from happening. Fishing and any other activities should give me the orbs automatically over time.