1. It seems that because my SA entity sells services (performed in the South Africa) to my USA entity, it has a nexus here, and thus need to file taxes. Your SA corporation might have a nexus in the US not because the customer is located in the US, but because you as an employee or manager of the SA corporation perform working activities physically in the US.
The location of the customer generally has no effect on the nexus.
Due to property devaluation is made a loss so that will not incur taxes or penalties. Right?
The corporation doesn't realize neither a loss nor a gain because the property value is changed. The loss or gain is realized only if the property is sold.
To determine if there was a gain or loss - the tax return should be prepared.
If the tax return was required and was not timely filled - the minimum penalty for a return that is over 60 days late is the smaller of the tax due or $135.
This SA based entity is often managed from here (in the USA) by myself.
That fact actually constitutes the nexus.
Looking at your last paragraph; How does this fact affect my ability to have it charge the USA entity for services rendered by my admin staff in SA?
That fact doesn't affect the ability of the SA corporation to charge for services.