Comma or semicolon for genuine "thank you" at the end of a sentence?

Speaking as an editor I can say that, of the two options you offer, either could be more meaningful and appropriate depending on what you are responding to. I’ll discuss both, therefore, so that you can decide in the context of the conversation at hand, and I will add a couple of further observations or suggestions beyond that.

Structurally speaking, the problem rests on whether your statement is effectively one sentence or two. I’ll explain…

First, this crucially comes down to whether your ‘thank you’ is there merely to convey politeness, or is actually a statement in itself. Although that distinction might seem minor, and perhaps tricky to make, it is the key to your Question.

You might be responding to what amounts to a query, even if it is not directly articulated. If your correspondent has signed-off with something like ‘Does that help?’ or even ‘That’s what I think, if it’s any use’ (that is, an implied query), for example, then a comma works best.

That is because, conventionally, ‘thank you’ after a comma primarily adds an indication of social courtesy to your response to someone, beyond simply giving information. In such cases, ‘thank you’ is an example of what linguists call phatic communication, defined on a British Council web page as ‘verbal or non-verbal communication that has a social function, such as to start a conversation, greet someone, or say goodbye, rather than an informative function’.

Obvious examples might be ‘Yes, thank you’ or ‘I’ll try the red, thank you’ (even if the question has not been asked out loud). In these cases, ‘thank you’ says nothing about the observable world of objects and events, but conveys an appreciation of someone else's interest or attention, adding nuance to an otherwise bluntly factual statement. Even ‘No, I’m OK, thank you’ politely acknowledges someone’s concern even while declining their help.

If your context is more straightforwardly conversational, though, the simplest way to start thinking about your Question is to note that both ‘Thank you’ and ‘It does help’ could perfectly well stand alone as individual sentences. If your intention is to confirm that someone has been helpful, and then to offer gratitude as a statement in itself, then of the options that you offered the semi-colon is better.

We can start with the (perhaps) underlying two-sentence structure ‘It does help. Thank you.’ Replacing the full stop with a comma then just converts the whole thing into what is known as ‘a run-on sentence’, which is an error.

Guidance from Walden University puts this succinctly:

A run-on sentence occurs when two or more independent clauses (also known as complete sentences) are connected improperly. […]One common type of run-on sentence is a comma splice. A comma splice occurs when two independent clauses are joined with just a comma.

Examples could be ‘That must be new, it’s really clean’ or ‘I’ve already finished, I’ll go home now’. One difficulty is that the reader can quickly have trouble understanding where the main sense lies. At the extreme, that kind of unending construction could go on for pages, which is perfectly OK in some novels, but probably not for what you have in mind.

Walden goes on to suggest:

Inserting a semicolon between independent clauses creates a grammatically correct sentence. Using a semicolon is a stylistic choice that establishes a close relationship between the two sentences.

If your intention is to connect two statements closely, and not simply convey politeness, then of the choices you offered the semi-colon is the way to go.

(It is even possible to suggest a colon as well, but that is beyond the scope of your Question!)

I can see why you might worry about a possible perception of sarcasm. Overemphasising such a response certainly could show that the purported courtesy is intentionally insincere. ‘No, really: I always wanted this to happen, thank you.’ You probably don’t face that problem here, though.

If you still feel that the recipient might misinterpret you in some way, however, then the best solution to that is to think about your own phrasing and make it definitive.

As a closing suggestion, then, personally I would revert to the two-sentence structure that you essentially have there (in disguise), and say something like ‘That certainly helped. Thank you!’ If someone can misinterpret that, then the problem is not your punctuation.