When submitting a disavow file, oftentimes people also disavow great links that help rankings, and not just the bad links.  For some site owners, identifying the links that should be disavowed (spammy links or links that were paid for in some way) versus the great natural links.  And sometimes those great links are really helping ranking and get disavowed by accident.

Gary Illyes made a great comment about using disavows when you notice rankings drop after disavowing – start removing the less shady links from the disavow file.

That said, there is always the possibility if the links are fairly new that Google hasn’t identified them as bad links yet, so even those bad links could be temporarily contributing to rankings before Google begins filtering them.  In these cases, especially in competitive market areas where you are likely to have competitors file spam reports against you, it is still smart to leave those in a disavow file to protect against manual actions – or assume that potential risk of leaving them live and not in a disavow.

John Mueller also commented when someone said there would be a “significant time delay” in Google using those links for rankings again – he said this isn’t true and Google will begin counting those links again once “recrawling & indexing / reprocessing” of those pages has been done.

This is something Google has said before on many occasions.  When asked to confirm again, he did.  But he also added that spending time on a per-link basis might not be the best way to spend time for a site, and to think bigger and long term instead.

So if you do notice your rankings drop, check the disavow for higher quality links that may have accidentally been included, then start removing the “less shady” links.