חשבתי שהיא לא תבוא, אבל היא כן באה.

Because Hebrew usually keeps the tense that matches the time of the event itself, not the English-style backshift of tense.

At the time of the thought, her coming was still in the future, so Hebrew says:

חשבתי שהיא לא תבוא

Literally, that is something like I thought that she will not come, but the natural English meaning is I thought she wouldn’t come or I thought she wasn’t going to come.

Because the second clause tells you what actually happened in the end.

• תבוא = will come
• באה = came / did come

So the speaker is saying:

I thought she wouldn’t come, but she did come.

If the event were still in the future, then אבל היא כן תבוא could mean but she actually will come.

It is the same word as yes, but here it is not answering a question. It is being used inside the sentence as an emphatic positive marker.

It pushes back against the earlier לא.

So:

• היא באה = she came
• היא כן באה = she did come / she came after all / she actually came

This use of כן is very common when correcting or contradicting a negative expectation.

Yes, you can leave it out:

חשבתי שהיא לא תבוא, אבל היא באה

That is still correct. But כן makes the contrast stronger.

In this kind of sentence, כן normally goes before the verb or predicate:

• היא כן באה = natural
• היא באה כן = not natural in this meaning

So כן usually sits where it emphasizes the truth of the statement.

ש־ means that.

It introduces a subordinate clause after verbs like think, say, know, hope, and so on.

So:

• חשבתי = I thought
• שהיא לא תבוא = that she wouldn’t come

Together:

חשבתי שהיא לא תבוא = I thought that she wouldn’t come

In writing, ש־ is attached directly to the next word, so ש + היא becomes שהיא.

Sometimes Hebrew can leave out the subject pronoun if it is clear from context, but here keeping היא is very natural.

There are two good reasons:

1. Clarity
   In תבוא, the form can be ambiguous in some contexts, so היא helps make it clear that the subject is she.

2. Contrast and emphasis
   In אבל היא כן באה, repeating היא gives a stronger contrast: but she, in fact, did come.

So the repetition sounds natural and helps the sentence feel balanced.

Good question. באה can indeed be either:

• present feminine singular: she comes / is coming
• past 3rd person feminine singular: she came

Hebrew often relies on context to tell you which one it is.

In this sentence, באה is understood as past, because the speaker is contrasting an earlier thought with the actual result:

I thought she wouldn’t come, but she did come.

They are not the same.

• לא תבוא = she won’t come / she wouldn’t come
• לא באה = she isn’t coming or she didn’t come, depending on context

So לא תבוא is clearly future-oriented.

By contrast, לא באה can be:

• present-like: she isn’t coming
• past: she didn’t come

In everyday Hebrew, present forms are often used for scheduled or planned future events, for example:

היא לא באה מחר = She isn’t coming tomorrow

But in your sentence, לא תבוא fits better because it expresses an expectation about a future event from the point of view of חשבתי.

Yes. It sounds completely natural in standard spoken Hebrew.

It is a very normal way to express:

• an expectation that turned out to be wrong
• a contrast between what I thought and what actually happened

The especially natural part is the pair:

• לא in the first clause
• כן in the second clause

That pattern is very common in Hebrew when you want to say I expected no, but actually yes.