I've moved your question to the Adobe Photoshop General forum. This is the best place for Photoshop questions.
What I do when flaterning layers changes the look, is to add a copy merged layer at the top of the stack Shift Ctrl Alt e (Shift Cmd Opt e). The flatern and al will be well.
Thank you Trevor, but I'm sorry, maybe my little note didn't contain enough information. When I mentionned merged layers, it included those obtained with the shortcut. So, the problem is still there