We faced a similar problem, but ours began to happen after everything was functioning properly.
What we found out is that for some reason a record appeared in the core_config_data table where there is a path "general" (without anything after it or maybe "/ general /") ...
The point, since it was one of the last entries, Magento sees this as creating (in this case, rewriting) the XML node "general" in core_config, which it builds, essentially destroying all other data in this branch of the XML object.
If you find this entry in the table, you must backup the table (always be safe) and delete this entry. Then clear the cache and you need to make sure that everything is back to normal.
We never determined HOW the record appeared in the table, but this was a fix for us.
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