Press Ctrl+S as it is usual for all applications. It is the command Saved Merged Changes in menu File on using toolbar/menu mode, or the purple floppy disk symbol in toolbar with tooltip Saved Merged Files(s)... on using toolbar/menu mode, or Saved Merged Files(s)... item in menu File on using ribbon mode, or Save merge changes on ribbon tab Edit in group Merge.
It is of course only possible to save plain text files. UltraCompare cannot edit Microsoft Word documents or PDF files.
Best regards from an UC/UE/UES for Windows user from Austria