I'm short on a source (and trying to dig up the correct old threads here would be a pain) but in addition to the "750 mile rule" PRIIA also constrained the system to existing endpoints as of that time [1]. Now there's been some debate as to the exact form that restriction takes...in their PIPs, Amtrak seriously examined, outside of Congressionally-specified new route studies, the following:
-A re-route of the Star via Charlotte (which would involve significant "new" trackage);
-An FEC-operating section of a Silver train (which would be a new section and operate over new track but not have a new endpoint);
-Re-instituting the Desert Wind in conjunction with the Zephyr (much the same as the FEC section above);
-Adding through cars from the Capitol Limited to the Pennsylvanian (much the same as above, but also tinkering with a "state" train);
-Sending the Cardinal to STL and/or sending a section to STL (which would involve a new or added endpoint); and
-Breaking several trains into two day trains (with forced overnights at an middle location, something which would technically have added mid-route endpoints to the trains in question [2]).
In none of these cases were PRIIA restrictions indicated as a problem. The language in the bill did, I believe, only refer to existing endpoints (ORL qualifying per the Sunset Limited only being "suspended"), but per the above examinations it seems clear that there's some flexibility: Re-routing existing trains between existing endpoints is clearly kosher, and adding sections with different endpoints as long as they're "bolted onto" existing trains seems allowable.
With all of that being said, the present fiscal environment seems likely to can this. If Amtrak were running $30m ahead of budget this year they might have trouble arguing the point but they're well behind budget instead. The one way I could see something happening here if funding proves to be hard to come by is if Wicker succeeds in loading a "thou shalt run the bloody train" amendment (think Byrd and the Cardinal, though this might have some conditionals attached to it) onto a funding bill in the future.
[1] BOS, NYP, WAS, LOR, SAV, SFA, ORL, and MIA on the East Coast; CHI, NOL, and possibly SAS in the Midwest; and SEA, PDX, EMY, and LAX on the West Coast
[2] ATL on the Crescent and BUF on the Lake Shore