Hi @ben,
Definitely not a one-stop shop. There are many steps, each with its own troubleshooting peculiarities. We should really compile a single forum post to help navigate the process!
Oh that's a tough one — I am not sure we have had to troubleshoot that step before, since usually filtering or merging is where the big issues happen. Maybe you could upload the qzv of your dada2 stats?
Filtering has nothing to do with overlap — at that stage the reads are still being filtered independently. Rather, you were not trimming enough on the reverse read (but trim more and then you have overlap issues).
No, unfortunately I do not even think the dada2 R tutorial has info like this, though the FAQs cover some of this.
Let's tackle problem 1 first: your denoising loss issue, then maybe you or someone else could give us a hand to tackle problem 2: putting together a step-by-step dada2 troubleshooting guide!