So what are the best ways of fixing lens flare in gimp? I've tried localized fixes, but I always get rough transitions between the fix and the rest of the picture.

Example issue with lens flare:

I've downloaded it. If you don't mind I'm gonna see what I can do with it.

select the effected area
go to colors>map>rotate colors and try and make the effected area all one shade if possible then go to colors>hue and saturation and you should be able to get rid of most of the flare areas. Of course you may need to touch up with clone tool or curves tool also.

Or what about using resynthesizer, that works well with that sort of thing.

Good idea Molly.

Thanks...Sometimes if it leaves a few artifacts, you can run unsharp mask and that helps too.

Thanks for the tips! I've never used rotate colors before...definitely will have to play with that.

That would work well for the circular flares, but what about large ghosting columns on the right and left?

If you are talking about that smoky look, I wouldn't take that out. I love it.

That seems to be the light shining through naturally. I would either try color > color balance and select highlights and play with red around 5 and blue about 7 or 12. Or leave it the way it is after using rotate colors.

I wanted to include the xcf too but it's 313mb so it probably doesn't fit here.

Good job!

Nice job EK. I still liked the look of the natural light shining through. It gave a nice early morning look. You did a good job on the lens flares.

Those two green circles is the lens flare they were getting rid of. Nice job of the brightness and contrast though.

I see molly. Shows you how much I know. Will look out for it in future.

Sallyanne, you are doing great and coming along like a house on fire.

Cool Sallyanne, I love that script, it works well in getting rid of wires, eg telephone and electrical wires etc. too

Thanks for the tip. I will be using it a lot more now I can see what it does.

I really could have spent more time on it and got the one in the bottom left better but I ran into a couple of issues with my comp not liking files that size in gimp. It kept crashing on me. I ended up having to scale it down quite a bit just to work on it and once my layers piled up it got worse. That's why usually my xcf are all merged down to just a couple of layers.