import re
repl1="k1"
repl2="k2"
p = r'(CN=Root,Model=.*,Vector=Reactions\[).*(\],ParameterGroup=Parameters,Parameter=).*(,Reference=Value)'
test_str = "CN=Root,Model=MYMODEL,Vector=Reactions[SOMEREACTIONS],ParameterGroup=Parameters,Parameter=PARAMETER,Reference=Value"
result = re.sub(p, r'\1%s\2%s\3'%(repl1, repl2), test_str)
print(result)
aW1wb3J0IHJlCnJlcGwxPSJrMSIKcmVwbDI9ImsyIgpwID0gcicoQ049Um9vdCxNb2RlbD0uKixWZWN0b3I9UmVhY3Rpb25zXFspLiooXF0sUGFyYW1ldGVyR3JvdXA9UGFyYW1ldGVycyxQYXJhbWV0ZXI9KS4qKCxSZWZlcmVuY2U9VmFsdWUpJwp0ZXN0X3N0ciA9ICJDTj1Sb290LE1vZGVsPU1ZTU9ERUwsVmVjdG9yPVJlYWN0aW9uc1tTT01FUkVBQ1RJT05TXSxQYXJhbWV0ZXJHcm91cD1QYXJhbWV0ZXJzLFBhcmFtZXRlcj1QQVJBTUVURVIsUmVmZXJlbmNlPVZhbHVlIgpyZXN1bHQgPSByZS5zdWIocCwgcidcMSVzXDIlc1wzJyUocmVwbDEsIHJlcGwyKSwgdGVzdF9zdHIpCnByaW50KHJlc3VsdCk=