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We have analyzed the reported issue (LoadEJResourcesFromAssembly results in error when hosted in server.) in our sample and we are unable to reproduce the issue in our end. We have prepared a simple sample and hosted it in server by enabling EJ Resources from Assembly. The embedded resources are loaded properly. You can find the details in the below screen shot.
For your convenience we have attached the same sample in the following location.
Kindly check with the sample. If still you face the problem then please share us the issue reproducing sample in which we can able to resolve the issue. If possible please share us the video clip or screen shot of the issue. Also please provide us the sample link which you have hosted in server. This will be helpful for us to server you better.
Thanks for your update.
Please let us know if you have any other queries.