We have finally managed to reproduce this problem and fixed it.
The following build should fix the problem immediately: http://jiraeditor.com/builds/jeditor-1.5.49-preview.jar.
Public 1.5.49 will incorporate this fix. It will be shipped within several days.
We are sorry for this inconvenience.
If you can see the templates on the Prepopulation tab in JEditor Configuration, but can't see them in Templates tab after upgrade to 1.5.47 do the following:
1. Uninstall JEditor 1.5.47
2. Download and install JEditor 1.5.46
There's a bug in upgrade script that sometimes makes templates inaccessible. The templates are not lost, they are stored in your JIRA DB. After downgrade you will be able to access them.
The fix of this issue will come with JEditor 1.5.48.
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