I would make a virtual clone of the terrain you have. Then recheck the elevations at the problem structures and I would even add a new modification on top of that modification. The next thing I would do is the basic dumb RAS debugs like save and close and reopen, disassociate that geometry with said terrain, save close reopen, rename the terrain save close and reopen, change the culvert invert to allow the model to work run it for a short duration and then go back and adjust back save close reopen…I know this isnt much help but we all know RAS is buggy as hell sometimes