I edited .jwmrc-tray to add a tray at the top of the desktop. When I had gotten it looking like I wanted, I restarted JWM then I opened JWM Desk Manager to change the icon layout. I selected "Bare-No Desktop Icons" thinking this would remove all of the icons but leave the two trays. It did remove the icons, but also both trays.
I looked at .jwmrc-tray again, and all my edits had been removed, but without any backup. The original pre-edit state of .jwmrc-tray was left (bottom tray), but the bottom tray was not there.
I double-checked .jwmrc, and it still contains an "include" for .jwmrc-tray.
(Fossapup64 running in Virtualbox with 8GB ram and 80GB virtual hard drive. Host is BionicPup64 with 32GB ram.)