Yes, you have to be very careful when using embedded SQL and fetching into an external DS.
There is no level check on external data structures, Your program will run with out notification of a level change. You may get a SQL mapping error but it wont cause an error message.If you are updating files, your going to have a long night.
There will be lots of problems if the program isn’t coded properly. Otherwise, it should be fine. You don’t show any relevant code nor give any indication what errors were seen (or “issues”), so it can only be guesswork. One common mistake is to code SELECT * FROM… instead of a proper select-list.