I recently had bamboo laid using Bostic’s Best glue. Long story short, the installer used a blue Scotch Brite pad to remove some of the glue spots left (the long story) on the surface. This left surface scratches and ruined the sheen on the areas he tested. My question is since these aren’t truly ‘scratches’ (my opinion), can they be buffed out and what method?

They did test a poly over one of these areas which did cover the scuffs, but that board appears slightly different in reflected light and I don’t think I will care for this as a fix overall unless we can find a better match. But even still it's not that orignal AlOx protective finish.

I wish I found this forum prior to the install and appreciate all the knowledge I’ve already gained. I hope those same experienced people have some advise for me.

It's your installer's problem to solve. Tell him to come here and ask questions on recommended repairs.

Their solution is to poly over all the marks. I'm not crazy about their method although their use of carb cleaner to get the glue off surprised me.
But if they were to post here, what would you suggest?

If the finish has been dulled down by the installer scrubbing it with an abrasive pad, perhaps the sheen could be renewed by an automotive rubbing compound. Applying poly in spots is a recipe for disaster unless they are going to coat the whole floor. But then that would void your finish warranty. Replace the worst ones would be the typical way to repair it I would think.

Board replacement

Board replacement seems to be very difficult task with the Bostic glue and the board being tongue and groove. I'm not sure I have confidense in the installers to do this well. That said I agree that would be the best solution.
If I ask this of them, what process should I listen for to know they aren't going to make things worse.
I realy appreciate everyones help with this situation!

If they are not confident or experienced at board replacement, have them hire someone who is. On a factory, prefinished floor, the typical method of repair is to replace the damaged board/s. This will keep the warranty in force and is the recommendation of most manufacturers and inspectors. They damaged the finish, it is their responsibility to make it right. If they do not want to replace or cannot find someone to do it, then withhold money from the final payment to cover the cost of replacing the damaged boards. Then ask the distributor for some references to floor repair craftsmen.

Very good points and I thank you for you input. Unfortantatly they have been paid in full. At the time of payment, the only problem was glue spots which they were confident where all coming up with the Goof Off. And thats where the story gets worse....