When i was using pinta my layers dissappeared
If my answer is correct (above), I have found a bug report on this issue (actually I reported a bug/wish a year ago): https://bugs.launchpad.net/pinta/+bug/1428720 to remove support of closing down pads from within pads itself, because it can be easily done by mistake. To turn off pads I suggested to only have View | Tool Windows.
It sounds like you should submit a bug, along with more steps about how to reproduce the issue.
Also check if you haven't accidentally turn Layers off. Check the menu View | Tools Window | Layers.
P.S. You should write your Pinta version from Help | About and operating system name/version.
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