When you save an Illustrator file in certain formats, the native transparency information is retained. For example, when you save a file in Illustrator CS (or later) EPS format, the file contains both native Illustrator data and EPS data. When you reopen the file in Illustrator, the native (unflattened) data is read. When you place the file into another application, the EPS (flattened) data is read.
When possible, keep your file in a format in which native transparency data is retained, allowing you to make edits as necessary.
Native transparency data is retained when you save to the following formats:
AI9 and later
AI9 EPS and later
PDF 1.4 and later (when Preserve Illustrator Editing Capabilities option is selected)
Illustrator flattens artwork when you perform any of the following actions:
Print a file that contains transparency.
Save a file that contains transparency in a legacy format such as native Illustrator 8 and earlier, Illustrator 8 EPS and earlier, or PDF 1.3 format. (For the Illustrator and Illustrator EPS formats, you can choose to discard transparency rather than flatten it.)
Export a file that contains transparency to a vector format that does not understand transparency (such as EMF or WMF).
Copy and paste transparent art from Illustrator into another application with both the AICB and the Preserve Appearance options checked (in the File Handling & Clipboard section of the Preferences dialog box).
Export in SWF (Flash) or use the Flatten Transparency command with the Preserve Alpha Transparency option selected. This command lets you preview how artwork will look when exported in SWF.