Since FEMA has a Detailed Study, there's will govern for regulatory purposes, unless you issue a Letter of Map Revision (LOMR).
Go to the FEMA website. Request the raw data used by the original consultant who did the HEC study. Sometimes, you get lucky, and the actual electronic file is available. But they always have printouts. Cost is nominal, usually $200 or so.
Recreate their sections or issue a LOMR, depending on whose sections best describe the current existing condition. from your name, you appear licensed; you will have to seal the data for the LOMR.
The original STUDY is almost certainly on HEC2, not RAS. HEC2 and RAS do the same things, RAS is just easier to use. You don't have to rerun it in HEC2; if it is electronic, RAS will convert HEC2 data nicely. If it is a printout, key it into RAS - but for that, you will need to learn to read HEC2 well enough to translate. That's probably what your friend meant.
HEC2 is also freeware, from the USACOE, same place you got the RAS software.
You can just explain the delta on the datum, because you probably can't adjust the roadway design datum, and your FEMA submittal will have to use their datum. Just explain in your H&H study for the bridge, correct for it and show the actual water depth is after the correction.
Remember: The Chinese ideogram for “crisis” is comprised of the characters for “danger” and “opportunity.”
-Steve