Something weird is going on with my bass drum batter head.

Do you know if 3M Command strips will leave residue if left on a surface for 2+ years?

That, I don't know. I don't have a lot of experience with the Command strips but by the way they get removed, I would think you'd be ok.

Another idea would be to use double sided tape like @C. Dave Run mentioned, but put thin strips of it between where the hoop and flesh hoop make contact. Like he said, the tape is thin and wouldn't affect how the drum tunes. And being in that spot, no one would ever know it's there.