So if you were to connect the two sides of a balanced output into a single-ended input, and both components had 3-prong ac plugs, you would be grounding one of the two balanced signal outputs. Depending on the design of the output circuit, that could conceivably cause damage.
To clarify my statement a little further, if both amp & powered sub had 3-prong power cords, the path by which the negative (black) output of the amp would be grounded is: Amp black to sub chassis ground to sub ac safety ground to safety ground pin on sub power plug, then via ac wiring to ac safety ground pin on amp power plug, then to amp chassis ground.
Also, I'll add to my previous comments that another way in which sub signal ground could conceivably become common with ac safety ground is if an internal short were to occur within the sub amp. That is very unlikely if it is well designed, but if a short were somehow to develope between its signal ground and the neutral prong of its 2-prong ac power plug, that would create such a situation since ac neutral and ac safety ground are tied together back at your ac service panel.
Regards,
-- Al