I got some new pick ups. Took a lot of work to get the pick up covers off my old stock pick ups, but I did it.

Now I find that the magnets in one of the two don't align with the holes. A very quick google said this isn't uncommon.

Will it affect the sound? I can deal with the aesthetics, but if it affects the sound then sad face.

I do plan on wax potting them.
That picture is way too big man.

It won't effect the sound any more than putting a cover on an uncovered pickup (arguably) does.
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