There should not be any problem.
I've never tried this for a BDC program, but feel, it is like any other program for background job.
You should try and see the results, in Dev client.
1.Try directly from SE38 (Program --> Execute --> Background)
or
Through a Tcode given to the BDC program (Program --> Execute in Background)
or
Create a variant to program and configure a background job through SM36, using this variant
(with periodic values of 2days).
Jogeswara Rao K