Does listening to a source in polarity reversal can cause any damage to one of the componentsNo, absolutely not.
Although some issues can arise if you have a separate powered sub -- let us know if you do and I'll address that further if necessary.
I'm wondering if the fact that you heard such a major improvement might mean that your speakers were previously connected out of phase relative to each other. Having the two speakers connected with different polarities, relative to each other, will cause a dramatic reduction in bass, as well as vague, diffuse imaging.
If what you just did was to change the polarities on BOTH speakers, then you indeed simply corrected for the pin 2 and 3 inconsistency, which I would not expect to produce such a major difference.
If on the other hand what you just did was to change the polarity on only one speaker, then you corrected what would have previously been a difference in relative phase (between channels), which would have produced the symptoms that you seem to be describing.
Regards,
-- Al