Hello Grace,
Did the error message show that you have a missing.rte file?
Nevertheless, you are correct, that it might be an issue as there should be multiple.rte files.
Can you do a little bit of troubleshooting: open your reach shapefile and check, how many reaches are in the attribute table. Now open the project database, locate the "rte" (I do not recall the exact name) table and check, how many entries are there?
Best,
Natalja