My immediate suggestion would be that by changing the assembly name of the log4net assembly, you somehow broke its type resolution, possibly for a logging configuration.
Keep in mind that your type names are now different.
This means that the type name, for example
log4net.Appender.RollingFileAppender, log4net
now will be
log4net.Appender.RollingFileAppender, new
(or something similar)
Check the logging configuration, fully qualify any applications, layout templates, etc. (basically the names of the log types in the list) to indicate a new assembly.
Also, if your logging configuration is in your web.config or app.config file (as opposed to a separate file), then the section definition will also need to be changed:
<section name="log4net" type="log4net.Config.Log4NetConfigurationSectionHandler, log4net" />
will become something like
<section name="log4net" type="log4net.Config.Log4NetConfigurationSectionHandler, new" />
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