Actually with haeme, and or flavin containing enzymes it is known for the 
cofactor to undergo reduction.
There is a recent JACS paper that explores these changes as a function of X-ray 
exposure.
(2012) J.Am.Chem.Soc. 134: 2823-2834
Excellent work done in part at Allen Orville's X6A
As far as quality of your data goes, unless your crystal is suffering from 
radiation damage (they all do!) from those free electrons/radicals
then your data should not be affected by the bleaching.
HTH.
Yuri

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