Did you change the the area graphics in any way, editing bits in or out? If you didn't, you should leave the reference to the original AR0906 TIS.
The reference to the TIS is in the WED. The main TIS of the area is the first overlay listed in NI. To change, you'd choose that overlay, select "View/Edit", then update the value of the TIS in the window that pops up. BUT, if you're changing the tileset, you don't want to use AR0906 as the name of your WED, because that will screw up the appearance of the actual AR0906. (Though it sounds like you're already changing this.) You might as well rename the whole kit and caboodle when you're first making/editing and saving your new area in IETME or DLTCEP in that case.