Now there's a question that has been asked in Photoshop circles for as long as I can remember. The ultimate answer, though, is that it's really up to you. Everyone will choose one or the other for different reasons. In the past, I used to flatten everything. Why? Because in most of the videos and book tutorials I have seen for photography that's what was shown. So like most humans who initially learn by imitating others that's what I did.
A couple of advantages to flattening layers are 1) it keeps your file size smaller; and 2) it looks cleaner in your layers panel. However, I recently discovered a problem, at least for me, after I have flattened my layers, and I'm really putting myself out there with this so please go easy on me... I can't always remember what I have done to the image! There I said it, and I suspect that I'm not alone out there on this.
I'm finding that the combination of using a number of different plug ins and masking techniques for different parts of the image, I don't always remember which filter I used, or what I painted back in or removed etc. So if I flatten my layers all of the information is lost to me, unless I remember, which as I mentioned above was my issue.
There are a lot of ways to organize your layers such as merging them, naming them and creating layer groups, so I'm beginning to do that instead of flattening. I'm not worried about file size as I have a lot of storage space. But now I can at least see what I have done.
So there it is... my answer to the question is not to flatten. How about you?
Cheers!
DC
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