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What if I used the Brother MFS for incoming faxes like labs, then used software to convert to OCR (like ABBYY or OmniPage)..could the documents then be routed through Updox so that they can be directly sent to the pts. chart (and also send me a message in my inbox that I have something to review?)

UpDox has no way of knowing which fax belongs to which person. Either way you're going to have to lookup the person whose chart you want to import the fax into. This will be the same for the Brother MFC or a faxboard.