After I updated some plugins online, when open one of my previous file, it shows such error.
If I press "OK", some contens in the file are missing.

How to fix it?

This message should appear if the file structure is corrupted/malformed. Hard to say without the file, but you can check with the previous program version if the problem is related to the file or the cutrent program version (instructions to setup a portable version are here).

Wrote

This message should appear if the file structure is corrupted/malformed. Hard to say without the file, but you can check with the previous program version if the problem is related to the file or the cutrent program version (instructions to setup a portable version are here).

Thanks for the tip.

Today, I used the 0.99.7610 portable version (it has been used for more than two months) to open the file,it was fine.
Then I updated some plugins (without upgrading to the latest beta version) through extension manager.
When I opened the file again, it shows the error message.