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Option 1 - File System
The application directory will be located somewhere like this on Windows...
{installation drive}:\usr\sap\{instance}\j{##}\j2ee\cluster\apps\Nakisa\{Nakisa Application}\servlet_jsp\{Nakisa Application}\root\
On *nix drop the "{installation drive}:" and change the back slashes to forward slashes; assuming "usr" is mounted at root.
The XML files will be in various sub directories in the delta of your build. Assuming you are on a single tenant system the path to the sub directory structure would be something like this.
{installation drive}:\usr\sap\{instance}\j{##}\j2ee\cluster\apps\Nakisa\{Nakisa Application}\servlet_jsp\{Nakisa Application}\root\.system\Admin_Config\__000__{Build Name}\.delta\
From there you should be able to find the location for the OTF files but you may need to copy any non-modified ones in from the level alongside the .delta (only changes are in the delta). You may also need to modify some of the other files to accommodate any of the OTF changes.
Option 2 - Export/Amend/Import
Export the published build from AdminConsole, un-zip it, amend the files (you could get any files not included in the delta by extracting them (e.g. via 7-ZIP) from the installation SCA), re-zip the build, import the build into AdminConsole.
Be Safe
In both cases good practice would be to take a back-up in AdminConsole, apply the changes to a new build (based on the currently published build) and publish the resulting build.
Hope that helps.
Regards,
Stephen.