What version of Photoshop are you using? I just took a layered image I had and flattened it and it didn't affect the transparencies. Obviously, you can't edit it after it's flattened.
Maybe you can merge layers that don't have transparencies together. Layers add alot of weight to the file size, how many do you have in your image?
I am using CS2. All the files in question have just one layer. Were there multiple layers I would merge them into one. My understanding of the term flattening as used in Photoshop is to force everything into a background layer which at the same time destroys the transparent background and forces it to whatever you have set at the time as your background color.
I think you are not understanding what I am working with or my terminology. I am working with seamless texture tiles. some that we sell utilize transparent backgrounds so they can be placed on top of other components in building an image and allow portions of the background to show. When you flatten an image, that transparency is lost.
I am attaching a sized down example of what I am working with (500 x 500 vs 3600 x 3600). It is a fence with a transparent canvas or background. The PNG version is 146 KB and the PSD version if 971 KB or more than 6 times larger.
The files open identically in Photoshop and the only difference is that PNG files utilize lossless compression. The problem again, is that Flexi does not support PNG but does support PSD. We would like our files to work in Flexi as we would like them to work in as broad a range of popular applications as possible. The new TIFF standard is not a usable solution for our situation because Flexi opens it but misinterprets the transparency as black. So I am researching whether or not distributing PSD files is a viable option for us with our seamless tile collections. The typical saved file sizes at 3600 x 3600 for PSD, one layer images ranges from 40 MB to 80 MB. The same file saved as PNG, ranges from 4 MB to 15 MB. The sizes for either format are affected by how much content is transparent.