Start Adobe Illustrator CS6 and open your .ai file by clicking File -> Open… Under the “Files of Type” drop-down, select "Adobe Illustrator (.AI,*.AIT)". Browse to the folder where you stored your .ai file, select it, and then click the “Open” button.
Your artwork will load and then you need to click File -> Save As… Under the “Save as Type” drop-down, select "Adobe Illustrator (.AI)". Name or rename your file and click the “Save” button.
On the next screen you will have a couple of decisions to make. Under the “Version:” drop-down you have options to select version 3, 8, 9, 10, all previous CS versions or even JI 3. I also check “Create PDF Compatible File”, “Use Compression” and “Embed ICC Profiles” if needed. Once you have everything set the way you want, you can click OK.
If a dialog box appears stating that “Saving this document in an older format may convert all type to point type and may disable some editing features when the document is read back in. Do you want to continue?”, you can just click OK, but make sure that you have kept the original CS6 file and have not overwritten it.
This is a fairly common occurrence for version formats not being backward compatible, but most of the time the effects are unavoidable.
Your new exported file is now ready to use.
P.S. About EPS problem:
- Illustrator saves every Illustrator EPS together with the Illustrator fork of the selected or current version.
- EPS flattens transparency. When you place an EPS in any application including Illustrator you get a flattened version of that file without transparency.
- When you open an EPS which is saved from Illustrator in the same version or a newer version of Illustrator you get the transparency back, not because it is an EPS as EPS does not support transparency but because the Illustrator fork is included in that file which is used by Illustrator.
- You can open an Illustrator EPS and resave as PDF/AI. This will create a file with transparency. This transparency is also alive when you place this file in applications which support transparency, like InDesign, Photoshop, Illustrator, etc.
- When an EPS is saved in a newer AI version either the EPS part is used or it is not possible to open. You get a flattened artwork without transparency.
- Illustrator is not a common PDF editor. The same is valid for EPS too. You will encounter the same problems you encounter when you open an non-Illustrator-PDF as you do with a non-Illustrator-EPS.
- You can convert any EPS in Adobe Distiller to a PDF. But be aware, even if the EPS has transparency information included in its AI fork, this information is lost by converting via Distiller. A Distiller PDF can not include any form of transparency.
- If you choose to convert an EPS in Distiller and you are aware about the transparency issues (as it is not a problem with older EPS or Freehand EPS or Corel EPS) use a setting which include all used fonts (they need to be available), turn off any image compression and image resampling and fit size to EPS content, and avoid any conversion of colors.