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When I update Infobase from EDT it shows me the following message:

"Properties' has been modified, but is still open elsewhere with identical changes. Closing this will not lose those changes. Would you like to save now anyway?"

I'm confused. Properties of what? Closing this? What is this? I am not closing anything. I keep pressing "Yes", but I want to understand what exactly I am doing.

Hello, Alexey!

I will clarify this this with developers and let you know.
Can you provide configurations before and after changes for us to be able to reproduce this issue? You can send it to int@1c.com.

I have sent you eclipse workspace.

Thank you, maybe the problem will be solved after clicking in main menu Project and then Clean...

Sorry, I gave up. I was trying to Clean.., to re-import from source with new workspace, to edit src files so EDT could read them without problem... but after several hours of struggling and receiving null-pointer exceptions I moved to old fashion designer and build everything from scratch, just copying the code. It was times faster than make eclipse work again.

Sorry for that, Alexey.
The developers are investigating the issue.