Hi Daniel Glen, thanks so much for responding, I understand a bit better now what is going on.
Is there a reason that 3dresample removes the oblique orientation information from the header? I know it doesn't make a difference for the AFNI display, but it does make a difference in analysis pipelines, especially with other software (e.g. ANTS). For instance, I applied a transformation that correctly registered an image to the original functional, but then failed to register it to the resampled functional. Actually worse than that: it didn't give an error but it produced a clipped version of the transformed image, because now part of the image was out of the (non-oblique) field of view. It was a long road to track that down and I imagine I may not be the only one to naively assume that 3dresample would conserve the header information.