It might have been clearer if you'd described what "a.vbs" and "b.vbs" were doing, but on the assumption that if "a.vbs" is taking a long time then it's the one that you want to run the file monitor, and only once a week. As you can't currently trigger the file monitor from a script, how about setting the "ScanOnStart" to true as you shutdown once a week and then at shutdown switch it off if it's on. I believe this would have the desired affect. The file monitor settings are stored in "MediaMonkey.ini" here...
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...so for me I have the whole "Music" folder monitored, but only the "_Downloaded" folder at startup. It's the "ScanOnStart1" and/or "ScanOnStart2" which would need to be modified for me. Does this make sense?