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As far as I know, there isn't a way to keep track of which flags you've used. Assuming you started around the 740000/800000 area though you could navigate there in a hex editor and find '29' bytes, as they signify setflags in scripting. Of course not every 29 would necessarily be a flag.
There isn't a way to keep track. But a good tactic is to just keep a txt file of all the flags you use, Jambo made a tutorial for extending safe flags and vars. So look at that.