...wow, did you just pwn yourself?
you HAVE to get much higher quality cotton buds to clean your sensor than the common variety that is available at the supermarket.. those would cost slightly more at certain pharmacies. haven't gotten new ones in a while so not sure where to get them now.
next, checking visually to check whether there are sharp objects is NOT ENOUGH
you have to use a blower to blow it for quite a while, BEFORE using sensor cleaning liquid to lessen the chances of stray fibres being left behind on your sensor and getting dragged around. even then, take note of the type of sensor cleaning fluid that has to be used - best to buy eclipse from visible solutions, they have 2 versions, one for something to do with tin-oxide in certain models, one is for older models. it seems that if you use sensor cleaning fluid on your 400d you have to use e2 instead of original eclipse.
that said, i won't worry too much about "scratching" the sensor per se, it is most likely a fibre left behind by your fooling around.
the stain could also be because of various reasons - perhaps you touched the cotton bud tip before you used it, perhaps whatever cotton bud you are using has some chemicals on the tip.. in any case you display a lack of confidence in handling sensor cleaning - i suspect later on if we do not suggest that you leave it to techs there will be more threads in future with possibly more severe problems (like using too much sensor fluid and letting it go UNDERNEATH the filter.. loads of things can go wrong with wet cleaning). it is probably best you send it in to canon, and see what happens; if you have scratched your sensor you must have really, really missed out big time on some particles on the tip.. though of course the filter covering the sensor isn't *quite* that easy to scratch, honestly.
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