I downloaded and installed Enable Media Replace Version 2.9.3, by Mans Jonasson. It works fine on my test system; I was able to replace one JPG image with another and did not get any error messages of the type you report. I tested this from the “Replace Media/Upload a new file” button on the Edit Media screen as well as the “Replace media” link on the Media/Library screen.
MLA does not have any interaction with the Enable Media Replacement plugin that I know of. Note, for example, that the “Replace media” link does not appear in the rollover actions of the Media/Assistant screen.
The “You do not have sufficient privileges to access this page.” message has nothing to do with file/folder permissions. It is issued when a user does not have the right WordPress Role or Capabilities to perform the action requested, or when the request does not appear to come from a source WordPress considers legitimate.
If you are logged in with an Administrator-level account and getting this error, there may be a problem with the plugin. There is a check_admin_referer
call in the EMR plugin code that would give you the error if the check failed.
You could try disabling the Media Library Assistant plugin and see if the problem still occurs. If so, it is an issue with the Enable Media Replace plugin. If the problem only happens when MLA is enabled, let me know and I will investigate further.
I will leave this issue unresolved until I hear back from you. Thanks for your interest and for your understanding.