...ok, trying to clear things up here, from the beginning before too much confusion builds up...
...you trying to "flatten" transparency to be able to print the file, and flattening from within illustrator...
>>> "i thought i had to flatten image for the printer" <<<
...is this a commercial print provider or your own desktop printer?
...either way, flattening typically occurs in the print stream (i.e. behind the scenes) when printing to postscript or saving to EPS format and is not required to be performed from within illustrator itself (unless in very particular circumstances)...
...flattening also occurs when saving to PDF (Acrobat 1.3) (file > save as), any version higher than 1.3 maintains the transparency inside the PDF...
...so in other words, flattening does not takes place in PDF versions 1.4 and higher. However, with a PDF of version 1.4 or higher your commercial print provider needs to support this format in their workflow, so that flattening takes place much later down the line (in their RIP before final output occurs)...
...this is why i'm unclear as to why you are having to flatten transparency from within illustrator itself...
>>> "i'm unclear what you mean when you say i have to flatten it to the object it's interacting with" <<<
...in your initial post, you mention that you lose transparency when trying to flatten a live paint graphic, i took the view you had a transparent effect applied to the live paint object and in turn it was on top of something else...
...when directly trying to flatten that selected live paint graphic the transparent "appearance" disappeared, which it will do, unless you select both the transparent object and the object underneath, so it knows what to flatten to, and maintain the "appearance"...
...anyway, with all that aside, trying to flatten transparency inside of illustrator is rarely required. This brings me back to my question above...
...is this artwork for a commercial print provider or to print to your own desktop printer?
andrew