1. depending on weather, bondo isn't suggested for much more than surface issues because it doesn't shrink/expand at the same rate as wood, so if you have cold winters and hot summers it's a very temporary fix. Wood filler would be better.

2. If the damage has extended more than halfway through the material, it should be replaced. Sistering is an option, but honestly for something visible (as opposed to floor joists underneath the floor), that doesn't end up looking very good. It may be possible to replace the entire length of lumber so that it just looks a bit newer than the others. It really depends on what you want and how much work you're willing to have done. Most pergolas I've seen would be able to have a few sections removed without becoming structurally unsound.

As with all things I've said in here, I am not to be taken as the 'final word' on anything you're experiencing, as there are always situations and particulars that I'm not familiar with and someone who can be there in person would be much more able to tell you your options.