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I didn't say to run sed twice; I said to run sed once using the global substitution twice. Running that global substitute twice will take care of ALL occurrences of the pattern you said you wanted...

Another solution is to just run your global substitution twice:
sed -e 's/|\.|/||/g' -e 's/|\.|/||/g'
which, with your latest sample input:
123.5|ABC.|.|.|.
234.4|DEF|.|.|.|.|.|
produces the...

With the g modifier, what matched once is out of scope for another match.
But a loop can do it
sed '
:L
s/|\.|/||/
tL
'Another solution is perl: by using a look-ahead an RE substitution with g...

$ sed "s/\.|/|/g" file
123.5|ABC|||.
234.4|DEF||||||

This doesn't really satisfy the "requirement to replace consecutive occurence of same string", it only removes full-stops.

Strange... tryawk 'NR==FNR {T[$1]=$2; next}
{for (i in T) if (2 <= gsub (i,"&")) {
gsub (i, T[i])
...

Previous solution optimized:
sed 's#.*#s,&,2g#' FILE2.txt >FILE2.sed
sed -f FILE2.sed FILE1.txt >RESULT.txt
Now an awk solution that does not do a RE substitution, but a substitution word by word:...

Assuming GNU sed....

Create the sed file using FILE2.txt:

sed 's#\([^,]*\),\(.*\)#s/\1/\2/2g;t#' <FILE2.txt >FILE2.sed


Use that FILE2.sed as the commands for sed:

sed -f FILE2.sed...