I did a little searching and didnt find any info on this, but when I ran the CF Mystic Updater so I could play with flex 2.0 and ColdFusion, I ran into a problem. I use the multisever install and although all the new files get posted in the correct location it is unable to update the web.xml to add the /flex2gateway/ servlet mapping.

In the installation log I found that it was trying to update the web.xml located at

c:JRun4wwwrootWEB-INFweb.xml

Those familiar with the differences between cf multiserver and cf standalone will recognize that path as the one for cf standalone, except with jrun instead of coldfusionmx7.

Anyway, I just created the wwwroot folder and WEB-INF folders and copied my web.xml from a valid cf intance into that folder. When I ran the updater the second time this file was updated correctly. Then I just copied it back into the webroot of my cf instances and I was good to go.

I hope this may help someone searching for a solution, as I was :)