mjhjmtu

1st file contains:

#. This is the file name to process: waveheight.txt
#. This is the latest data to process if exists: waveheightNew.txt
 FilNam=Project2128/Input/waveheightNew.txt
 if [[ ! -f $FilNam ]]; then FilNam=Project2128/Input/waveheight.txt; fi

2nd file contains:

#. This is the file name to process: waveheightBin.txt
#. This is the latest data to process if exists: waveheightNewBin.txt
 FilNam=Project2128/Input/waveheightNewBin.txt
 if [[ ! -f $FilNam ]]; then FilNam=Project2128/Input/waveheightBin.txt; fi

Now I need to process the files by changing .txt to Bin.txt?
Using sed "s/.txt/Bin.txt/" will lead to BinBin.txt for the 2nd file.
By sed "s/Bin.txt/.txt/" and then sed "s/.txt/Bin.txt/" seems awkward.

Would it be smarter to skip the unwanted matches?

You could include the Bin in the text to replace if there which would then result in it being replaced with itself:

sed 's/(Bin)0,1.txt/Bin.txt/g'

Or if your sed supports EREs with -E (or -r for some older versions of GNU or busybox sed):

sed -E 's/(Bin)?.txt/Bin.txt/g'

Beware . is a regexp operator that matches any single character. You need . to match a literal dot.

You can use a perl negative lookbehind to match .txt, but only it it's not Bin.txt.

perl -pe 's/(?<!Bin).txt/Bin.txt/g'

Hence, to test:

$ echo 'Bin.txt foo.txt' | perl -pe 's/(?<!Bin).txt/Bin.txt/g'
Bin.txt fooBin.txt

Unfortunately, sed does not offer this construct.

You may do a conditional substitution with sed, for example, you may test whether the line already contains Bin.txt and only perform the substitution if it doesn't.

sed '/Bin.txt/!s/.txt/Bin.txt/'

This assumes that there will only be need for one substitution per line.

You may also do the substitution unconditionally, and then correct it if it went wrong, as you hinted at in the question, but in the same call to sed:

sed -e 's/.txt/Bin.txt/' -e 's/BinBin/Bin/'

You could do this with GNU-sed as shown:

echo "$Filnam" |
sed -e '
 s/.txt/n&/;T # try to place a newline marker to the left of .txt, quit if unsuccessful
 s/Binn/Bin/;t # If the marker turned out to be just to the right of Bin => Bin.txt already 
 # existed in the name, so we needn"t do anything n take away the marker n quit
 s/n/Bin/ # Bin could not be found adjacent to .txt so put it n take away the marker as well
'

### Below is the POSIX sed code for accomplishing the same:
sed -e '
 s/.txt/
&/;/n/!b
 s/Binn/Bin/;/n/!b
 s/n/Bin/
'