Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę?

It means regardless of that or, more naturally in English here, regardless of whether.

In this sentence, niezależnie od tego, czy... czy... is a very common pattern meaning:

• regardless of whether ... or ...
• whether ... or ...

So:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę? = Are you calling regardless of whether you have an overpayment or an underpayment?

The phrase is built like this:

• niezależnie = independently / regardless
• od = of / from
• tego = that

But as a whole, you should learn niezależnie od as one expression: regardless of.

Because od requires the genitive case, and to in the genitive becomes tego.

So:

• to = this / it / that
• od tego = of that / from that

In the full structure:

• niezależnie od tego, czy... = regardless of whether...

Polish often uses tego in this kind of bridge phrase before a clause. English usually does not translate it word for word.

Compare:

• Nie jestem pewien tego, czy... = I’m not sure whether...
• To zależy od tego, czy... = It depends on whether...

So tego is part of a very normal Polish structure before czy + clause.

Because Polish often uses czy ... czy ... to mean whether ... or ....

So:

• czy masz nadpłatę, czy niedopłatę = whether you have an overpayment or an underpayment

This is different from English, where we usually say whether ... or ..., not whether ... whether ....

Polish examples:

• Nie wiem, czy przyjdzie, czy nie. = I don’t know whether he’ll come or not.
• Niezależnie od tego, czy jesteś zmęczony, czy nie, musisz skończyć. = Regardless of whether you’re tired or not, you have to finish.

So the repeated czy is completely normal.

Yes, it is the same word, but here it functions as a subordinating conjunction, not as a question particle.

Polish czy can do two common jobs:

1. Question marker

   • Czy dzwonisz? = Are you calling?

2. Whether/if inside a larger sentence

   • Nie wiem, czy dzwonisz. = I don’t know whether you’re calling.

In your sentence, both instances are the second type:

• niezależnie od tego, czy masz nadpłatę, czy niedopłatę

So here czy means whether, not just a question marker.

Because Polish usually does not need subject pronouns when the verb already shows the person.

• dzwonisz = you call / you are calling
• masz = you have

The endings already tell us it is you singular.

So ty is normally omitted unless you want emphasis, contrast, or clarity.

Compare:

• Dzwonisz? = Are you calling?
• Ty dzwonisz? = You’re the one calling? / Are you calling?
  (more emphasis, surprise, contrast)

So in a neutral sentence, leaving out ty is normal.

Because they are in the accusative singular.

The verb mieć (to have) takes a direct object, and that object usually goes in the accusative:

• masz nadpłatę
• masz niedopłatę

The base forms are:

• nadpłata = overpayment
• niedopłata = underpayment / shortfall

These are feminine nouns ending in -a, and in the singular accusative they change to -ę:

• nadpłata → nadpłatę
• niedopłata → niedopłatę

This is a very common pattern for feminine nouns:

• kawa → kawę
• książka → książkę
• sprawa → sprawę

These are billing/account/payment words.

• nadpłata = overpayment, meaning you paid too much
• niedopłata = underpayment, meaning you paid too little / there is an amount still owed

The prefixes help:

• nad- often suggests over / too much / above
• niedo- often suggests under / not enough / insufficient

And both words are related to płacić (to pay).

So these are especially common in contexts like:

• utility bills
• bank/account settlements
• taxes
• invoices

It is grammatically present tense, but in English it could be translated in different ways depending on context:

• Do you call ... ?
• Are you calling ... ?
• Will you call ... ?
  sometimes in practical instructions/context

The verb dzwonić is imperfective, so it can describe:

• a present action
• a repeated/habitual action
• a general instruction, depending on context

Without more context, Dzwonisz...? could sound like:

• Are you calling...?
• Do you call...?

If this comes from customer-service instructions, it may even function like:

• You call whether you have an overpayment or an underpayment.

So Polish present tense is often broader than a single English tense choice.

Because Polish uses czy ... czy ... instead of czy ... albo/lub ... in this structure.

English says:

• whether X or Y

Polish often says:

• czy X, czy Y

So the second czy effectively carries the meaning that English expresses with or.

You generally would not say:

• niezależnie od tego, czy masz nadpłatę albo niedopłatę
  in the same way, because that changes the structure and sounds less natural for this exact pattern.

The standard pattern is:

• niezależnie od tego, czy X, czy Y

Yes. That is a very common alternative.

These are close in meaning:

• niezależnie od tego, czy...
• bez względu na to, czy...

Both can mean:

• regardless of whether...

For example:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę?
• Dzwonisz bez względu na to, czy masz nadpłatę, czy niedopłatę?

Both are natural.
A learner can safely treat them as near-equivalents in many contexts.

A small note:

• niezależnie od sounds a bit more formal/abstract
• bez względu na is also very common and natural

The given word order is natural, but Polish word order is fairly flexible.

The original:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę?

You could also put the longer phrase first:

• Niezależnie od tego, czy masz nadpłatę, czy niedopłatę, dzwonisz?

That version is also grammatical, but it may sound more marked or more like you are focusing strongly on the condition.

In ordinary speech, the original order is smoother and more conversational.

So the word order is not completely fixed, but some versions sound more natural than others.

After niezależnie od, you use the genitive.

Examples:

• niezależnie od pogody = regardless of the weather
• niezależnie od sytuacji = regardless of the situation
• niezależnie od tego, czy... = regardless of whether...

In your sentence:

• od tego is genitive
• tego is the genitive form connected with to

So a useful pattern to remember is:

• niezależnie od + genitive

It would be:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę.

That means:

• You call regardless of whether you have an overpayment or an underpayment.

The difference in writing is just the question mark, but in speech the intonation changes too.

As a question:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę?

As a statement/instruction:

• Dzwonisz niezależnie od tego, czy masz nadpłatę, czy niedopłatę.

This kind of present-tense statement is common in instructions and customer-service language.

Sometimes in loose English, yes, but whether ... or ... is better.

Why?

Because Polish czy ... czy ... clearly presents two alternatives, and English whether ... or ... matches that structure best.

So the most accurate translation is:

• whether you have an overpayment or an underpayment

Using if is possible in some English contexts, but it can sound less precise:

• regardless of if you have...
  This is understandable, but many learners will benefit from remembering:
• czy in this kind of structure often corresponds to whether, not just if.