Hydraulic Profiles not Generating - Database issue- Drainage ORD

I recently had to update the trunkline for a drainage network. I am updating the hydraulic run to outfall but when i click the prompts, I get an exception log. 

If I use the hydraulic run from node and click the last node and click the outfall it follows the old layout

I have redrawn the conduits, but i am still getting this error. I have compacted the database and resynched the drawing also, but these issues are still persisting. 

 When i do the model integrity check i get these errors (see photo below) It looks like there is some miscommunication between the database and links, I am unsure how to remediate these issues.

Is this file salvagable? I am apprehensive to start new file from scratch because there are quite a few custom feature definitions being used for different sized manhole bottoms. 

Thanks, 

Emily