ERC20 contract method balanceOf returning wrong data

I am creating a contract to help migrate old ERC20 tokens to an updated ERC20 tokens.
I was running a test for the migrate method i've created

    function migrateTokens() public payable {
        uint256 totalBalance = _deprecatedToken.balanceOf(_msgSender());
        require(totalBalance != 0, "Address not holding deprecated tokens");

        _token.transferFrom(address(owner()), _msgSender(), totalBalance);

the first line

uint256 totalBalance = _deprecatedToken.balanceOf(_msgSender());

is always returning 0.
But if i check the balance from outside the contract it is returning the correct number, but the issue resides in calling the .balanceOf method inside another contract

Extra info:
This is how i'am fullfilling the _deprecatedToken and _token variables

function updateToken(address updatedToken) public onlyOwner {
        _deprecatedToken = _token;
        _token = IERC20(updatedToken);

I am missing a core concept in this, please can i get some help here ?

Can you show the script calling the function to see if maybe there is an await missing, or if a parameter might be the cause?

Those are the metadata to complete the test

describe('TokenExchange', () => {

    let token: Token;
    let tokenExchange: TokenExchange;
    let trustedForwarder: MinimalForwarder;
    let owner: SignerWithAddress;
    let bot: SignerWithAddress;
    let user: SignerWithAddress;
    const tokenSupply = 1000;

    async function updateToken() {
        const updatedToken = await deploy(1000, trustedForwarder.address);
        await (await tokenExchange.connect(owner).updateToken(updatedToken.address)).wait();
        return updatedToken;

    async function migrateToken() {
        await (await token.connect(owner).transfer(user.address, 10)).wait();
        const updatedToken = await updateToken();
        const userBalance = (await token.balanceOf(user.address)).toNumber();
        await (await token.connect(user).approve(tokenExchange.address, userBalance)).wait();
        await (await updatedToken.connect(owner).approve(tokenExchange.address, userBalance)).wait();
        await (await tokenExchange.connect(user).migrateTokens()).wait();

    beforeEach(async () => {
        [owner, bot, user] = await ethers.getSigners();
        trustedForwarder = await deployTrustedForwarder();
        token = await deploy(tokenSupply, trustedForwarder.address);
        tokenExchange = await deployExchange(token.address, trustedForwarder.address);
        await (await tokenExchange.connect(owner).grantRole(tokenExchange.BOT_ROLE(), bot.address)).wait();

This is the test scenario that fails:

it('should migrate all address deprecated tokens to the updated tokens', async () => {
                const updatedToken = await updateToken();
                await migrateToken();

                expect(await token.balanceOf(user.address))

                expect(await updatedToken.balanceOf(user.address))

There is no reason why this would behave differently when called from inside another contract versus when called off-chain. There must be another problem. Make sure you're using the same token addresses.