Besides the "Chinese Taipei" vs. "Taipei, China" name use issue which seems to be resolved in favor of "Chinese Taipei," Beijing had one other trick up their sleeve. That's to place Taiwan in the
"Z" C section of the opening ceremony, while Taiwan has always been in the "T" section (as the official abbreviation for the team is TPE).
Edit: An anonymous reader makes a correction:
The Taipei Times has mentioned in at least four articles that the procession order will be based on "the number of strokes in the first character of each country's Olympic designation in simplified Chinese script."
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Under this system, Taiwan will be the 24th team to enter the stadium after Japan and before the Central African Republic and Hong Kong.
Some in Taiwan fear that this is will be used by Bejing as a future precedent. The Presidential Office has been very low key and just indicated it would be "difficult" to simply boycott the opening ceremony.
Coming in the wake of all the measures Ma has taken to placate Beijing, this seems like a real dickhead thing of the Chinese to do. As my wife put it, 「他們連這種小豆腐也要吃。」
It's probably too late to expect any sort of real protest from the Taiwanese side.