Are you editing the engines.cfg value on disk or using Aircraft Editor?
I don’t think the issue is changing Engine.0 = ...., but rather that AE makes edits to the files. You should have no issue actually making all the changes you need, but directly in engines.cfg as opposed to saving with AE.
If you place the Bell 407 files into the Cabri G2 SDK sample, then it will fly fine. Make any edit in AE and reload and you’ll find the NR decays and the aircraft doesn’t work anymore. When you look at the edits to engines.cfg and flight_model.cfg, you’ll find it made many changes to the files.
I never tracked down which edits are incorrect, but a few definitely look suspect. It’s a huge burden for devs to have AE mess up a working config, and then need to work backwards through all the edits to figure out what went wrong. So I would recommend using source control and using only the gizmo in AE but then saving values manually.
EDIT 1:
It removes RPM_on_TP_torque_table and n1_to_shaft_torque_table which is definitely required.
AE is just not compatible with helo-turbine at all. I’ll submit a bug.
EDIT 2: bug thread: Aircraft Editor destroys Helo-Turbine engine configuration