I want to only remove grouped commas from this csv to change the number of variables to two

Using perl instead of sed to get more advanced regular expressions:

perl -pe 's/(?:\G[^,)]*|\([^,)]*)\K,(?=.*?\))//g' input.csv c("4288" "57534"),MIB1 c("2272" "2385"),FHIT c("5550" "10531" "56239"),PREP c("25809" "23669"),TTLL1 

This will remove all commas that appear inside parenthesis.

Same solution I have answered here, that will also apply to your question with a bit modification here:

sed -E ':loop s/(\([^)]*),([^)]*\))/\1\2/; t loop' infile 

Breaking down:

Note: un-escaped ( or ) outside character class [...] is to used for grouping match; escaped \( or \) or within character class [...] will match literal ( and ); ^ is negation match, so [^)] matches "any single character but not a )".

then we have:

(\([^)]*): first group match, back referend \1 is referring to.
,: match a single comma.
([^)]*\)): second group match, back-reference \2 is referring to.

Considering one sample line like below and explaining on how this match works:

c(("4288", "57534", "somtoher")),d("f1", "f2", "f3"),MIB1 

this (\([^)]*),([^)]*\)) will match:

1. from very first open parenthesis ( followed by anything but not a ) and up-to last , to the first close parenthesis ); so, first group match \1 will match (("4288", "57534", part of the sample line at above;

2. then anything after last , to the first close parenthesis up-to first close parenthesis and ) itself will be in second group match \2; it will be "somtoher") part of the sample line above.

3. in replacement part in \1\2, we revert the both matched groups back but dropped comma between them.

4. :loop s///; t loop; do steps 1 to 3 in until all commas between (&) cleared in a sed's loop (loop is used as label).

   at first attempt, our sample line would change to:

   c(("4288", "57534" "somtoher")),d("f1", "f2", "f3"),MIB1 

   at second attempt would be:

   c(("4288" "57534" "somtoher")),d("f1", "f2", "f3"),MIB1 

   at third attempt would be:

   c(("4288" "57534" "somtoher")),d("f1", "f2" "f3"),MIB1 

   and so on.