Hi, @Elmata ,
For copying documents between site collections, you can use the built-in send-to button in the files ribbon. And you can even manage the copies in other site collections with the original one.
You can get more information about this feature here: https://support.microsoft.com/en-us/office/using-send-to-in-sharepoint-server-3fe1c568-021c-4c6b-a6c2-d55e6a3518de?ui=en-US&rs=en-US&ad=US
For the automatically copy file to another library with a flag, you may try to copy the file via Rest API in the workflow if not using any 3rd party solutions. As you have known, the built-in copy document action does not work cross sites. It will be tricky and complicated. Here is an example you can refer to: http://johnliu.net/blog/2014/2/19/using-sharepoint-designer-2013-workflow-to-copy-file-via-res.html
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