Let's say you stored your tools on a magnetic organizer in your toolbox, such as the one pictured.
Now you go and use a socket or wrench that is slightly magnetized. Have you done wrong?
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The answer: In most cases, no. There are a few exceptions.
The most common exception is when adjusting any sort of magnetic compass system. Flux valves, whiskey compasses, etc... are usually supposed to be adjusted with tools made of brass.
Even then, your typical A&P will adjust the whiskey compass, for example, wait for the thing to stop spinning like crazy, and then make a slight adjustment back the other way. He'll repeat that process until he gets it right. I'm not saying it's right, but it's what most of them do.
The only other scenario I can think of would be bringing those tools too close to a CRT-based display system. Magnetized tools can make the display go a little wacky.
There may be others, but that's all I can think of off the top of my head.