Hello all, this a bit tricky for me to explain, please bare with me.

I have Synolgy Drive Server running on my DSM with App portal setup.
I have a public domain pointing to an Nginx reverse proxy server. i have the proxy set to point to the port for Drive Server. so when my clients enter mydomain.net, they are taken straight to the Drive login portal rather than DSM login. that being said the 5001 port is not not accessible from public side.
the Drive Server functions perfectly this way.

However, when i do Create File Request in DSM, it creates the link using the DSM port ( mydomain.net:5001/share.... ) removing the port from the link results in a 404.
now if i change the reverse proxy to forward to 5001, the file request works fine. but users can no longer directly access Drive login without /?launchApp... added to the URL.

any ideas so that it work both ways would be much appreciated.

Leave the setup as you intended. When you get a link generated with 5001 port, just rename and correct the path using your reverse proxy acceptable url. Leave everything after the 1st / as it is. It will work that way no worries.

Synology Drive Admin Console -> Settings -> Others

Have you tried adjusting the settings in Customise Sharing Link?