Learn Hardcore German: Wir entdeckten zufällig einen Fehler im Vertrag, was hilfreich war. - We discovered an error in the contract by chance, which was helpful.

It refers to the entire preceding situation/event (the fact that we discovered a mistake), not to a single noun. So was hilfreich war means “which was helpful” in the sense of “the discovery was helpful,” not “the mistake was helpful.”

Could I say …, der hilfreich war instead of …, was hilfreich war?

No, that would mean “the mistake, which was helpful,” because der would refer to the masculine noun der Fehler. Unless you truly mean the error itself was helpful (unlikely), use was, which refers to the whole preceding clause. (If you want a full main clause instead, you can say: …, und das war hilfreich.)

Why is there a comma before was hilfreich war?

Because was hilfreich war is a subordinate (relative) clause. In German, subordinate clauses are separated by a comma from the main clause. The comma is mandatory here.

Why is the verb at the end in was hilfreich war?

In German subordinate clauses, the conjugated verb goes to the final position. So in the relative clause was … war, the verb war must appear at the end.

Is was here the same as the question word “what”?

No. Here was is a relative pronoun meaning “which/that,” referring to the whole event described in the main clause. It’s not the interrogative “what?”

Could I use welches or das instead of was?

welches: Not in this function. welches (like welcher/welche) is a relative pronoun for nouns, not for entire clauses. Using welches to refer to the whole preceding statement is considered wrong or at least very stilted.
das: As a relative pronoun, das also refers to a (neuter) noun, not to a whole clause. If you want to use das, make it a new main clause: …, und das war hilfreich.

Why is it einen Fehler (accusative) and not ein Fehler?

Because Fehler is the direct object of entdeckten. Direct objects take the accusative, and Fehler is masculine: nominative ein Fehler, accusative einen Fehler, dative einem Fehler, genitive eines Fehlers.

Why im Vertrag and not in den Vertrag or am Vertrag?

im = in dem (a contraction). It’s dative because it expresses location (where the error is) rather than motion.
in den Vertrag (accusative) would mean motion into the contract (e.g., “to put something into the contract”).
am Vertrag (“at the contract”) is not idiomatic for this meaning; use im Vertrag (“in the contract text”).

Is the preterite entdeckten natural here? Could I use the present perfect?

Yes. In written German, the preterite (entdeckten) is common. In everyday speech, the present perfect is more typical:

Wir haben zufällig einen Fehler im Vertrag entdeckt, was hilfreich war. Both are correct.

Where can I put zufällig? Are other positions possible?

Yes, it’s flexible:

Wir entdeckten zufällig einen Fehler im Vertrag. (neutral, very natural)
Zufällig entdeckten wir einen Fehler im Vertrag. (fronted for emphasis: “By chance, we discovered …”)
Wir entdeckten einen Fehler im Vertrag zufällig. (possible but less common-sounding) In general, placing zufällig early (after the verb or at the start) is most idiomatic.

What’s the difference between zufällig, zufälligerweise, durch Zufall, and aus Versehen/versehentlich?

zufällig / zufälligerweise / durch Zufall ≈ “by chance/coincidentally.” All work here. zufällig is shortest; zufälligerweise is a bit wordier; durch Zufall is a prepositional phrase with slightly stronger emphasis on the role of chance.
aus Versehen / versehentlich = “by mistake/accidentally” (implying an error you made). Not appropriate here because discovering a mistake wasn’t itself a mistake. Example: Ich habe die Datei aus Versehen gelöscht (“I accidentally deleted the file”).

Could I rephrase with stoßen auf or finden?

Yes:

Wir stießen zufällig auf einen Fehler im Vertrag, was hilfreich war.
Wir fanden zufällig einen Fehler im Vertrag, was hilfreich war. Nuances: entdecken = “discover/uncover (something previously unknown)”; stoßen auf = “come across”; finden = “find,” the most general.

Is hilfreich the best word? What about nützlich or vorteilhaft?

All can work, but nuances differ:

hilfreich: helpful (esp. for actions, information, circumstances) — most natural here.
nützlich: useful (often for tools/features, but also abstractly).
vorteilhaft: advantageous/beneficial (more formal, emphasizes benefit). Example alternatives: …, was sehr nützlich war. / …, was vorteilhaft war.

Why not say …, was hilfreich gewesen ist/war?

You can, but it sounds heavier and is rarely necessary. Simple past war is concise and idiomatic. Use perfect forms (gewesen ist/war) only if you need to stress completion/result in a particular time frame; otherwise prefer war.

Is there any stylistic alternative to the relative clause?

Yes. A clean alternative is a new main clause with a demonstrative:

Wir entdeckten zufällig einen Fehler im Vertrag, und das war hilfreich. This is slightly more explicit and conversational than the relative …, was … construction.