The goal of rarefaction is to subsample to an even sequencing depth. So, the fact that you have the same sequencing depth (in this case, 79000 sequences/sample which was probably your rarefaction depth) is exactly what you should expect.
The error message seems relatively self explanatory: “The following IDs are not present in the metadata”. If this is the case here, it may be an ongoing issue, so I would check your metadata throughly before proceeding.
Please refrain from editing in these kinds of questions after the fact --- it makes it difficult for us to address your original question, since hijacking like this turns the topic into a moving target (in my opinion). Next time, just open a new topic, or if you think it is relevant, post as a reply in the original topic. We get notifications when new posts and topics are created, but not when edits to random topics happen. This doesn't mean don't edit your post --- if you see a typo, a mistake, or something that you think can be clarified, by all means, edit away. Its when you start layering on new questions that makes it difficult for us. Thanks for your understanding.