Short answer. Yes, generally. If you fail, without justifiable cause, to comply with a court order to include an omitted necessary party, the rule treats that failure as a waiver of your claim against that party — though the rest of your case can still proceed against the parties already before the court.
What the law says
The failure to comply with the order for his inclusion, without justifiable cause, shall be deemed a waiver of the claim against such party.
Rule 3, Section 9 — Non. Read the full provision →
You have to explain the omission first
Section 9 does not assume every case names every necessary party from the start. If a pleading asserting a claim leaves out a necessary party, the rule requires the pleader to set forth his name, if known, and state why he is omitted. That explanation is the first checkpoint — it puts the reason for the gap on record instead of leaving the court to guess whether the omission was deliberate, careless, or simply because the party could not be identified or located.
The court decides whether the reason holds up
If the court finds the stated reason for the omission unmeritorious, it may order that the omitted necessary party be included — but only if jurisdiction over that person's person can actually be obtained. This is a judgment call for the court, not an automatic consequence of failing to name someone. A pleader who gave a genuinely sound reason for the omission should not expect an inclusion order at all; the risk described in the question arises specifically once the court has already ordered inclusion and found the earlier explanation wanting.
What happens if you don't comply with the order
Once the court has ordered inclusion, failing to comply without justifiable cause is deemed a waiver of the claim against that particular party. The emphasis matters: the consequence attaches to noncompliance with the court's specific order, not merely to the original omission. It also is not automatic in every case — if there was a justifiable cause for still not complying, the rule does not treat that failure the same way. But absent such cause, the claim against that one party is treated as given up.
The rest of your case is not lost
Non-inclusion of a necessary party does not stop the court from proceeding with the action as a whole. The case continues against the parties who are properly before the court, and the resulting judgment is rendered without prejudice to the rights of such necessary party — meaning that party's own rights are not decided or extinguished by a case they were never actually part of. So losing the claim against the omitted party under this rule is a narrower consequence than losing the entire case.