I found the cause. A tower reached 600 m, but a flag can only be planted 500 m or more from another player's claim. So a tower raised just outside your border could still reach your flag. While it was shooting at you, every hit stopped you hardening or repairing. That is what you were seeing, and it is what made "tower, burn the flag, plant in the hole, tower that" so easy.

I have cut tower range to 500 m, the same as a flag's claim. A tower can no longer be built close enough to shoot at someone else's flag. This is live now.

One case is still open. You can stand about 55 m from your flag to harden or repair it, so if you stand on the tower's side of the flag and the tower sits right at the edge of your claim, it can still reach you. Standing on the far side of the flag keeps you out of range.

If a tower hits you from further than 500 m now, tell me roughly where it is and I will look.