Learn Hardcore Croatian: Ako je bolesna, vjerojatno neće doći. - If she is sick, she probably will not come.

Because je is a clitic (the unstressed present-tense form of “to be”). Croatian clitics must appear in second position within their clause. In Ako je bolesna, the first stressed item is Ako, so je comes immediately after it. You cannot move the clitic to the end: Ako bolesna je is ungrammatical.

Can I say Ako ona je bolesna?

No. The clitic je must stay in second position, i.e., after the first stressed element. The correct version with an explicit subject is:

Ako je ona bolesna, … (OK)
Ako ona je bolesna, … (wrong)

Adding ona simply adds emphasis to “she.”

What exactly is je here? Could it mean “her”?

Here je = “is” (3rd person singular of “to be”). There is also a clitic je meaning “her” (accusative), but that appears with a transitive verb:

Vidim je. = “I see her.”
In your sentence there is no transitive verb, so je can only be “is.”

Why does bolesna end in -a?

It agrees with a feminine subject. Predicate adjectives in Croatian agree in gender and number with the subject:

Feminine: Ako je bolesna, …
Masculine: Ako je bolestan, …
Neuter (e.g., for dijete “child”): Ako je bolesno, …
Plural: Ako su bolesni (m. pl.) / bolesne (f. pl.), …

Do I have to say the pronoun ona (“she”)?

No. Croatian is a pro-drop language; the subject is usually omitted when clear from context. The adjective’s feminine form (bolesna) already implies a female subject.
Use ona for contrast/emphasis: Ako je ona bolesna (a ne netko drugi), vjerojatno neće doći.

Can I reverse the clause order? What about the comma?

Yes:

Fronted condition (comma required): Ako je bolesna, vjerojatno neće doći.
Condition last (usually no comma): Vjerojatno neće doći ako je bolesna.

Croatian typically uses a comma when the subordinate clause comes first; when it comes last, the comma is usually omitted.

Why is the present tense used in the ako clause for a future meaning?

In Croatian, time after ako (“if”) is normally expressed with the present tense even when referring to the future:

Ako je bolesna, neće doći. = “If she is ill, she won’t come.”

Alternatives and nuances:

Ako bude bolesna, … is also correct; it can sound a bit more prospective/formal.
Avoid Ako će biti bolesna in standard usage; ako će appears only in special cases implying volition/intention.
For the event of becoming ill, use a perfective verb: Ako se razboli, vjerojatno neće doći.

Where should I put vjerojatno (“probably”)? Does word order change the nuance?

Default/most natural:

Vjerojatno neće doći.
Ona vjerojatno neće doći.
Ako je bolesna, vjerojatno neće doći.

Less common or marked:

Neće vjerojatno doći. (possible, but feels awkward/afterthought-like)
Neće doći, vjerojatno. (colloquial afterthought)

Placing vjerojatno before the negated future (neće) is the neutral choice.

Is vjerojatno the same as vjerovatno?

Meaning: yes (“probably”).
Standard: In Croatian, the standard form is vjerojatno. Vjerovatno is standard in Serbian/Bosnian and occurs colloquially in parts of Croatia but is not the norm in standard Croatian.

What exactly is neće? How do I form the future tense here?

Neće = “will not” (3rd person singular of the future auxiliary htjeti as a clitic + negation). It combines with the infinitive:

Negative: neće doći = “will not come”
Affirmative word order: Doći će. / Ona će doći. (the clitic će also wants second position)

Note: In Croatian, to express refusal more clearly, use ne želi doći or neće htjeti doći. The pattern neće da dođe is characteristic of Serbian; it’s not standard Croatian.

Why is the infinitive doći used and not a finite form like dođe?

Future I in Croatian is formed with the auxiliary ću/ćeš/…/će + the main verb in the infinitive: (ne)će doći.
A construction with da + present (da dođe) is not used for the future in standard Croatian after će; it’s typical of Serbian.

Should it be doći or dolaziti?

doći (perfective) = a single arrival event: neće doći = “won’t come (on that occasion).”
dolaziti (imperfective) = repeated/ongoing: neće dolaziti = “won’t be coming (habitually/over a period).”

Your sentence predicts a single non-arrival, so doći is right.

Can I drop the verb “to be” and say Ako bolesna, …?

Not in standard Croatian prose. The present-tense copula (je/jesam…) is required: Ako je bolesna, …
Copula-dropping occurs in headlines or very telegraphic style, but it’s not standard in normal sentences.

Does the sentence talk about now or the future?

It can cover either, depending on context:

Present state: “If she is ill (now), she probably isn’t coming.”
Future/occasion-based: “If she is ill (at that time), she probably won’t come.”
If you want to make the prospect explicit, use Ako bude bolesna or the eventive Ako se razboli.

Can I use kad instead of ako?

They’re not interchangeable in meaning:

Ako = “if” (conditional, uncertain): Ako je bolesna, neće doći.
Kad/kada = “when/whenever” (temporal): Kad je bolesna, ne dolazi. (general habit: “When she’s ill, she doesn’t come.”)

Using kad changes the sentence from a one-time prediction to a generalization.

What’s the difference between je and jest?

Both mean “is,” but:

je is the normal clitic form (used here): Ako je bolesna, …
jest is the full/emphatic form, used for contrast or emphasis: Ako jest bolesna, svejedno će doći. = “Even if she is indeed ill, she’ll come anyway.”