When editing local storage and SD card files, Xodo is capable of appending to the original PDF. However, if you find Xodo is duplicating files instead of appending to the original one, here are some tips:
If you are opening file from another app to Xodo, there is possibility that the file manager app does not grant write permission to the file. In this case, Xodo will not be able to write back to the file, examples for such app will be the built-in Files app.
To solve this problem, you can open the file directly through Xodo's file browser, or download a popular file manager app that does allow other app to have write permission to outgoing files.
If you are suddenly having trouble saving documents to your SD card, please check to see if your SD card is corrupted.