I ran across this a few weeks ago.  All you need to do is restore your profile line in geopak, but in the direction opposite of what you did previously.  I can't remember whether it was upstream to downstream or vice versa but hec ras imports the sections based upon the direction geopak stores your centerline profile alignment.

Oh yeah, you also have to recut your xsections after you change the orientation of your profile line.

I meant to say "to flip XS in HEC RAS" .

I think my EZ-ist way is to use Geopak's cut DTM profile on each xs section location (I kept them in the DGN file thank jeebus) as flipped, store ASCII and paste into the X xsetion editor...but then the GIS cut lines are still wrong

Maybe.  In case you didn't know you can cut and paste to and from HEC RAS using control C (cut) and control V (paste).  To cut highlight necessary info and control C. To paste you must highlight at least as many blank cells as info stored and control V.  If you do this sort of thing on a regular basis though it might not be a bad idea to try storing the profile in a different direction and cut x sections (about 10 to 15 min. total time max using geopak road software) and write the geopak report out for import and have no more worries about data manipulation.  This may not be as easy in HEC RAS 3.0.  You know there is a free version of 3.3 available now.  I'm still using 3.2 and it is a fairly easy process.

BTW Does it matter what direction the XS are cut in, as long as they are all the same?

I guess it depends on what your client's ultimate use of the HEC RAS output will be.  For instance if they were submitting a model to FEMA for a LOMA or the like I would think they would want everything on the up and up.  Who ever will be inputing manning's n values for various locations along the sections would certainly need to know and then still it could be confusing.  There is additional input as well that could become confusing.  It is much better to match the real world incase somebody wants to make a site visit or look at the topo.  I believe the water surface elevations generated by HEC RAS would be the same because you have the same section and flow as long as all the other inputs take the reverse sections into account.

Not really from a hydraulic pov.  But Convention is important when presenting results and such.  I thought I saw a button or ? to flip those in HEC RAS.  Hmmm I cant seem to remember.  Oh well, I would change everything around however you can.  Stationing increases upstream and xsecs from left to right looking downstream.  Try to maintain the convention.  If you used a prog to cut the xsecs then it shouldnt take that long to recut them.

Here's what I did. Turns out Geopak DID cut the HEC XS correctly...well I re did the input files and imported the GIS geomtery into a blank HEC geometry window. I opened 'nother HEC RAS, with my project open. I went section by section and pasted the new info in...I'm glad the phone didn't ring o/wise I would have lost my place.

BTW this is an isolated bridge replacement. The end result of the HEC study is to show that the new bridge WSE is equal to or below the existing

As far as HEC-RAS calculations go, the software takes your cross-section Manning's values and your downstream reach lengths which approximate a 3-dimensional model and squish them down to a point-value for energy loss along the long section of the creek; for the purposes of calculation, you have a 1-dimensional model, so switching your LOB and ROB won't make any difference.

If you maintain convention with regards to your x-section stationing, you will be much better off when you, the reviewer, or any other engineer revisits the model; particularly if you add to the model at a later stage. It might also save you some extreme confusion while trying to do your bridge contraction and expansion calculations.

Theoretically if you document your break from convention in your model development report, you are okay... but who reads the model development report when there are fun HEC-RAS files to dig straight into?

Please note that the latest version of HEC-RAS is 3.1.3, not 3.3, and similarly, previous version 3.1.2, not 3.2!

In the Geometry Editor, under the Tools menu there is an option to "Reverse Stationing Data" (4th one down).  This lets you select which cross-sections to reverse stationing on.