The MATE panel is stored in two files, and is glitchy. The disappearance or misloading of the panel at reset is classic, in my experience.
The two files can be found in /usr/share/mate-panel/layouts by default, with extensions .layout and .panel for a single panel. These two files are created, with the names user-tweak.layout and user-tweak.panel, by saving a panel out using mate-tweak.
These can be edited by hand as text files to alter the panel, though the structure is odd, particularly the positioning counts.
Note also that if you want a panel to hide when not selected, mate-tweak mis-saves the files with the hide option unspecified in one of the files: it must be specified in both.
Below is a sample of typical general entries, rather than for panel objects; objects and positions are listed in opening entries for .panel, and are then listed with details in both files and must match:
/usr/share/mate-panel/layouts/user-tweak.layout:
[Toplevel bottom]
orientation=bottom
expand=true
size=19
auto-hide=true
/usr/share/mate-panel/layouts/user-tweak.panel:
[general]
default-layout='panel1'
object-id-list=['menu', 'launcher', 'windowlistapplet', 'showdesktopapplet', 'notificationarea', 'clockapplet', 'object-0', 'object-2', 'object-1', 'object-3']
toplevel-id-list=['bottom']
[menubar]
show-places=false
show-desktop=false
[toplevels/bottom]
expand=true
orientation='bottom'
screen=0
y-bottom=0
auto-hide=true
size=19
y=748
The only solution I have found for misloading panels in MATE is to set a panel at live build and stick with it, and never attempt to change, and/or rebuild the panel files from mate-tweak.
The command to set the current panel layout is also in gsettings:
$ gsettings list-schemas | grep panel
org.mate.panel.menubar
org.mate.caja.sidebar-panels.tree
org.mate.panel
org.mate.caja.sidebar-panels
$ gsettings list-keys org.mate.panel
confirm-panel-remove
locked-down
default-layout
object-id-list
toplevel-id-list
disable-force-quit
drawer-autoclose
enable-program-list
enable-autocompletion
enable-animations
tooltips-enabled
disabled-applets
history-mate-run
show-program-list
highlight-launchers-on-mouseover