Can we use $FLEX$ multiple times in a single Valueset?

Yes we can use :$FLEX$ multiple times in a single valuset.

Example.
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WHERE a.bank_account_id IN (SELECT b.bank_account_id
                              FROM CE_BANK_ACCT_USES_ALL b
                              WHERE b.org_id= :$FLEX$.XXST_OPERATING_UNIT1
AND (NVL(AP_USE_ENABLE_FLAG,'N' ) = 'Y' OR NVL(AR_USE_ENABLE_FLAG,'N' ) = 'Y' ))
AND   c.BANK_PARTY_ID = a.BANK_ID
AND  d.branch_party_id=a.bank_branch_id
and c.bank_name=:$FLEX%.XXST_BANK_NAME
and d.bank_branch_name=:$FLEX$.XXST_BANK_BRANCH_NAME

 Write above code in where condition box.

here XXST_OPERATING_UNIT1,
       XXST_BANK_NAME,
         XXST_BANK_BRANCH_NAME are previous valuesets which are already used for a concurrent program.

While creating valueset follow the standard rules like use XX in starting of name and use meaningful name as a valueset.