A DD file (GAMS data dictionary with sets and parameters declarations) is created for each selected "scenario" on the solve form. You must already be taking care of the order to control the overwrites. SysSettings deserves additional care.
One of the important functions of this file is to declare the default interpolation rules. These rules are not applied in SysSettings if an interpolation rule has already been set in BASE or SubRES. But they are applied to timeseries that carry interpolation rules declared in other locations.
To make sure that the default interpolation rule does not overwrite a specific one that you might have declared, it is a good idea to position SysSettings immediately after the SubRES on the Solve form.
A possible consequence: you might get $170 warnings if you have interpolation defaults for User Constraints in SysSettings, as they will be declared downstream. To get around this, I normally declare the interpolation rules along with the UC and keep them out of SysSettings.
Another recommendation: copy the stable choices of interpolation rules in the transformation files of BY and SubRES templates. This will simply reduce the data processing burden of SysSettings, which is processed far more frequently (each SYNC operation) compared to the BY and SubRES transformation files.
