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In the UI I for some reason have one Model and one Model.001 where the later on is corrupt. When selecting this screen the UI freezes and the only way to get out of it is to use the Ctrl/ keys.

The blend file is binary so I can't edit it out manually. Is there a way to remove this?

Blender 2.68a

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Reload startup file Ctrl-N (or any file, actually) not containing the corrupted screen layout. Reopen the problematic file but clear Load UI checkbox, under Open Blender File settings group in the file open dialog. Then save the file.

With Load UI unchecked, Blender will reuse UI settings from previously opened file, for the file to be loaded.

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I keep a small Python console open for these types of fixes:

bpy.data.screens['CorruptScreenName'].user_clear()

Note you must first leave the corrupt screen, e.g CTRL-LEFTARROW. Alternately, bind a key to:

bpy.ops.screen.delete()

see: https://developer.blender.org/T36175

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