Changing file extension in SharePoint behaviour when copying/moving file from different site

We are trying to modify the file extension in a document library in SharePoint. Our use case is to encrypt the file and change its extension to html. We are observing unexpected behavior when a file is being copied/moved from another site. In this case, certain SharePoint functionality is breaking such as FileHandler, etc. Refer the following screenshot for more details: Here, both files are converted into html but only the file that was uploaded is correctly detected by the FileHandler. 

Steps to reproduce:

1. Upload a docx file in any document library in Site1.

2. Move/Copy the docx file to a document library in Site2.

3. Upload a docx file in the document library in Site2.

4. Rename the docx file to html file using REST API.

5. Verify the behavior difference between both the files.

Expected behaviour:

There must be no difference in the behavior between uploaded files and moved/copied files.

Queries:

1. This issue has been observed recently. Has something changed that might have caused this?

2. Is there any API to force change the type of the file.