By way of explanation...
CMD reads (and does env var substitution), parses, and executes one top-level command at a time.
In your example, it reads the "for /f..." command all at once parsing and performing %var% substitution.
Once this is complete, it then executes the for loop, performing delayed !var! substitution.
Unfortunately, !var! substitution is not a do-substitution-until-none-left. This makes it hard (as in the answerer's solution) to perform the substitution into the !var:src=dst! value.
You will need a way that during execution you can get guaranteed substitution. This requires a for-statement, or something that involves reading and %var% substituting again. One way of doing this is to use the CALL :LABEL form where you can call to a specific label in your .cmd file and have this section do what you want:
...
call :GenS
...
and then:
:GenS
set S=!S:%T_DAY%=%EODNUM%!
goto :eof
BTW: I'm perplexed that you didn't notice the ECHO %EODNUM% not working in the loop as during the reading of the for loop all %var% substitutions are made.