(A) Any file called "temp" can be overwritten.
(B) There is an option on the middle menu above the workspace (under the RENAME options - near the bottom of the RENAME menu), to overwrite the chosen file (lets call it OVERWRITE-CHOSEN).
A typical use would be
(1) You have a file AAA to process on the Chosen-Files list.
(2) You process the file, name the output, BBB, and return to the workspace.
(3) At this stage your pre-processed file AAA is on Chosen-Files list, and your output-file BBB is at the top of the workspace.
(4) Highlight the output file (BBB) by clicking mouse on it (but don't alter the Chosen Files list!!).
(5) Use the OVERWRITE-CHOSEN option. This renames BBB to AAA (deleting the original AAA) effectively overwriting the original.
(C) This also works with BULK PROCESS. If you process 1000 files (so you have 1000 files on the Chosen-Files list) and hence you get 1000 NEW files at the top of the workspace, you can highlight those 1000 files and select the OVERWRITE-CHOSEN option, so that all original files are overwritten with all the new ones!!