While generally not recommended to remove multiplications with compartment sizes from kinetics, here is how it could be done. All it needs to work is the python libsbml package installed.

drop_compartment_multiplication.py

from libsbml import *

def replace_compartment_multiplication(node, compartents):
    """Removes all multiplications with compartment sizes from the given ASTNode.

    :param node: The ASTNode to process.
    :type node: ASTNode
    :param compartents: A list of compartment ids.
    :type compartents: list[str]

    :return: The new ASTNode.
    """
    # convert the ASTNode to an infix string
    infix = formulaToL3String(node)

    # add spaces around infix operators
    infix = ' ' + infix + ' '
    infix = infix.replace(')', ' ) ')
    infix = infix.replace('(', ' ( ')

    # remove compartment multiplications
    for c in compartents:
        infix = infix.replace('* ' + c + ' ', '')
        infix = infix.replace(' ' + c + ' *', '')

    # parse the infix string to an ASTNode
    return parseL3Formula(infix)


def drop_compartment_multiplication(input_file, output_file):
    """Drops all multiplications with compartment sizes from the given SBML file.

    :param input_file: The input SBML file.
    :type input_file: str
    :param output_file: The output SBML file.
    :type output_file: str

    """
    # read the SBML file
    doc = readSBMLFromFile(input_file)
    if doc.getNumErrors(LIBSBML_SEV_ERROR) > 0:
        print("Read Error(s):")
        doc.printErrors()
        return
    
    model = doc.getModel()
    if model == None:
        print("Model not found!")
        return
    
    # only replace compartments that have an id and 
    # are of size 1 (otherwise the result would differ later)
    compartments = [ c.getId() for c in model.getListOfCompartments() if c.getId() and c.getVolume() == 1 ]
    
    # replace kinetics
    for reaction in model.getListOfReactions():
        if not reaction.isSetKineticLaw():
            continue
        kl = reaction.getKineticLaw()
        if not kl.isSetMath():
            continue
        math = kl.getMath()

        # create a new ASTNode to replace the old one
        new_math = replace_compartment_multiplication(math, compartments)
        kl.setMath(new_math)

    # write the new SBML file
    writeSBMLToFile(doc, output_file)

if __name__ == "__main__":
    if len(sys.argv) != 3:
        print("Usage: drop_compartment_multiplication input-file output-file")
        sys.exit(1)
    input_file = sys.argv[1]
    output_file = sys.argv[2]
    drop_compartment_multiplication(input_file, output_file)