That is to be expected. You cannot move folders in the Finder that are indexed in the database without problems as DEVONthink cannot (yet) find them to reconnect. This is a know limitation that many of us have requested be changed, for some time now. Here is one thread on this that was posted just yesterday link. One thing that you can do to overcome this in most situations is to move the indexed folder into the database, move it inside another indexed group in the database, and then when the script is triggered the group will be exported back out as an indexed folder in the Finder, in its new location. More trouble than should be necessary to deal with this, but it does work.
Does the triggered sync script work as expected if you do not move any folders in the Finder?