How do I make Tracker ignore that directory? Aren't ALL the standard folders in MyDocs on emmc hidden by default (which has always struck me as totally weird)? If so, I don't think they'd get ignored, because the file manager does show them (Maemo stock fm shows them without a period, in Filebox it's there).
To edit tracker ignore list in a nice easy way install 'trackercfg' by nicolai. Through it you can set all trackers options.
If you stop tracker from indexing one of your sources, then you will have to rebuild the database evertime you want to switch sources.