This is a long-standing gripe.
QuickLayers is handled by an add-on (plug-in) and the palette arrangement stored in a WE does not include such things - or their visibility. PITR (pain in the rear).
You can put some (most?) of the QL functionality into a docked, custom toolbar.
I like the palette as it is, so just work around this annoyance by having a shortcut assigned to it to bring it back. Since ctrl-L (cmd-L) is Layers, I use ctlr-shift-L (cmd-shift-L) for QuickLayers...
One of the forum moderators • AC 26 USA and earlier • macOS Ventura 13.2.1, iMac Pro 10-Core, Radeon Pro Vega 64