Flattening is changing one letter of my font

This is an effect of outlining some fonts. Outlining destroys font quality, by design. Just don't outline. If you believe you really have to, please describe your reasons so we can help you find a non-destructive alternative.

Please explain what you mean by "flatten", exactly. In the PDF world it can mean at least three different things...

Also, what version of Acrobat are you using?

With your file open in Adobe Acrobat, go to "File"--->>> "Properties".

In the next dialogue window that will pop up, click on the "Fonts" tab and check the fonts used in the document.

You may need to manually embed the listed Font types. However, you may also need to  check if that particular  font type has any license restrictionsthat doesn't allow embedding. Otherwise I am thinking a unicode or alternate text issue.

You can find more with the Accessibility Tool. Run a full report and spot what are the failed tests. Then you can use this information to work around the problem with the Print Production tool --->> PDF Fixups ( I  am unsure if this will fix anything  but you should give it a try).