I can't answer this specific question, but I have been trying to work through some timer problems of my own. Searching for that application note has an interesting 2nd hit on the ST forums..

One user volunteers some sad truths about the documentation:

The timers' description in ST's materials is an incredible mess. Instead of one properly written chapter, dealing with all the features and pointing out those omitted in the lesser-capable timers, they inflated the UMs with several copies of the timers' description, plagued with factual errors, omissions, apparent copy/paste and forgot-to-delete-this errors - plus the basic text is still of very poor quality.

For the 'F4xx, which I use, I tried to write down some of the most obvious errors in a "doc errors" writeup, http://www.efton.sk/STM32/STM32F4xx_doc_errors.txt ; but as far as the timers' chapters go, I'd recommend ST to discard the existing and rewrite it from scrap.

For your amusement, for example, have a glimpse at Table 49 on page 363 in RM0313...

JW

Hopefully you find some answers in his errata... I have a lot of reading to do :/