I don't know why, but when I play the note A anywhere on the fretboard, it sounds horrible, especially on the 6th string. I'm not sure how to describe it but it sounds almost like if you played to the right side of a fret. This thing only happens when i use my fingers, when i use a pick every fret sounds fine. I don't know when it started, but the guitar was fine until a few days ago
One possible explanation is that something had gotten loose in the guitar, even at an almost microscopic level, and when it vibrated its natural resonance frequency was that of an A, possibly 110 Hz or 55 Hz. (That's A2 or A1, two or three octave lower than A4 = 440 Hz).
In this way, when you played As, that "something loose" resonated, creating the unpleasant result in the sound.
Removing the strings and putting them back had the effect of making that "something loose" settle again, therefore removing the sympathetic resonance effect.
That "something loose" might have been in the bridge, or perhaps in the machine heads, both things being in direct contact with and under tension from the strings. But it could also have been in the pickup, truss rod, or somewhere else.
If it happens again, try to listen carefully to different points on the guitar, and see where this sound really comes from, that will give you a clue.