Ive HEARD that not having enough backpressure from the exaust can sometimes cause problems with valves. That could cause an engine to run hot and damage it. Im no bike tech, so I dont know, but I will tell you that the pipe on my CBR is an RT1 and dosnt seem to have any form of baffle or restriction at all. So I really dont know for sure. Someone here will be able to answer this for you soon, dont worry!

Fox

 

I can't think of any way of causing damage or additional heat when you have the exhaust gases being removed faster than before.
If the muffler was blocked at some point before the baffle was removed then perhaps there might be a problem but even then I doubt it.
I'm surprised the headers are painted.
Maybe somebody else painted them with crappy paint?

 

Lean engines burn hotter. Removing bafflel cause a lean burn.
Are the exhaust valves burnt? Do a compression test. Other than that, you're good to go.

 

lus1:

If the engine is running lean enough to burn valves it should be noticeable while riding it and the muffler should be almost white. Pulling a plug would tell you immediately if it's significantly lean.
While removing the baffle _might_ lean it off bikes generally run rich enough for it to not be a problem.

lus1:
Ｉｆ　ｉｔ　ｒｕｎｓ　ＯＫ、　ｇｏ　ｆｏｒ　ｉｔ．　Ｂｕｔ　ｔｈｅｎ　ｇｅｔ　ｉｔ　ｓｏｒｔｅｄ　ｓｏ　ｔｈａｔ　ｙｏｕ　ｗｏｎ’ｔ　ｈａｖｅ　ｔｏ　ｗｏｒｒｙ　ａｂｏｕｔｉｔ　ｉｎ　ｔｈｅ　ｆｕｔｕｒｅ．

 

If the engine is running lean enough to burn valves it should be noticeable while riding it and the muffler should be almost white. Pulling a plug would tell you immediately if it's significantly lean.
While removing the baffle _might_ lean it off bikes generally run rich enough for it to not be a problem.