Good question. I tend to agree with your flood vendor; however, this sounds like something that should be directed to the experts at FEMA. If you email them through the link on their website, they generally get back to you with 48 - 72 hours and this sounds like the kind of straightforward question they can answer authoritatively. (If you don't get an answer here and you do go to FEMA, it would be great if you could post the response here.)
In the meantime, I don't think you have any choice but to start the 45 day process with these loans. The examiners will be all over you if you don't and perhaps a new LOMA -- if necessary -- can be completed in that time.
One question: If these properties are already in a flood zone, why was the area re-mapped? Logically, that doesn't sound like something FEMA would do. Are you sure somebody hasn't made a mistake there?
Good luck.
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The opinions expressed are mine and not those of my employer