No, this is just the limitation of handicap racing. 

It would have been in the. Nor and the boat chose to enter. So fault? 

I suppose it would be possible for a sufficiently biased RC to engineer class splits as to favour individual boats or classes, even more so if course selection and handicaps were brought into the mix. I do recall an incident where an RO said, when queried about a bizarrely penal handicap my class had been given for an event, stating that he had heard we had won everything at a major event a few miles away, and didn't want it happening at his club. What made this particularly amusing was that the style of course set for the first event particularly favoured our boats, and the style of course for this gentleman's event completely precluded such a happening.

I suppose if the bias were malicious and sufficiently egregious and blatant, it might just shade into misconduct under RRS69, although it seems a stretch. Maybe if there were significant cash prizes. But otherwise I agree with Michael, this is the nature of the game. Every -or at least most- dog has its day. Its not an improper action to set class splits or even courses that favour some boats over others for handicap events, indeed its pretty much impossible to avoid. 

Rrs 69 is against a competitoror suoport person, not a raceofficial. 

I'm not familiar with PHRF but I think IRC is a similar system, classifying a broad range of cruising and racing ballasted monohull keel boats for competition by providing ratings comprising single figure allowances based on time.  It provides the following guidance to race management.  "With the ever-increasing range of boat types racing under IRC, it is inevitable that courses and conditions will affect race results. Race Committees can minimise these effects by considering carefully the types of courses set. Conditions are beyond the control of a race committee, but even then course location may be significant. ... Noting also that a balance of course types is a fundamental part of fair yacht racing, it is strongly recommended that race committees should set a variety of courses. For IRC regional or national championships this should be stipulated as a requirement."  There  is more detailed comment in Section 5 of IRC Race Management 
As both a competitor under IRC and race official, I have no issue with conditions in some races favouring one type of boat over another, but in a series running over the course of a year, expect that every boat will have its day, provided the race official follows the guidance of setting a variety of courses. 
What can be an issue is the safety argument: on a day with marginal conditions, heavy boats could compete safely and do well but the race organisers abandon races because it is perceived to be unsafe for light boats (though some do cope well), and in light conditions, the light boats are favoured.  

You'll need to race under ORC in order to use a boat's polars plus have the Rc use the right scoring option in order to more fairly level the playing field. If you sign up to race under a flawed/simplistic , one-number handicap system you accept its inherent limitations.

With the essence of the question really being PHRS handicaps (or otherwise handicapping or rating systems for that matter), as wind and current changes are really ‘par for the course’, I can’t myself see any avenue in the RRS for a given protest committee to engage in such a protest and it would be found as ‘invalid’. Presumably, the boat owners were prior aware of their handicap and thus decided whether to race or not (RRS 3). 

Any further reviews or challenges by a boat owner over their given handicap must surely be directed to the applicable Authority and organisers.

As a matter of aligned interest, I have personally witnessed an inter-club-regions regatta recently here in the Philippines (PY handicapping): when the NOR was first issued – followed later by the SI document, it stated four (4) separate classes (Racing. Cruiser-Racer, Classic Cruisers and Multihulls), but due to inclement weather external to the venue, and boats stuck back in those ports, at the last-minute the organisers combined the limited standing boats into a single mixed-fleet (all four classes combined) and a ‘quick-fire’ amendment was issued accordingly. All standing-competing boats agreed to continue to race. As the NOR allowed for it, and in the spirit of things, there were some handicap adjustments made on the second day by the RM-RO (some systems like SailSys can even do such adjustments automatically – up to preset percentage ranges), based on the performances from the first day. No protests on that matter were raised.

For PHRS (and most handicap or rating systems really), the published intent ([representations]} is generally one of: “PHRF is a performance handicapping system for keelboats designed to facilitate open and fair competition between boats…” and “…the handicapper must always favor the fleet and not an individual boat. The theory being: If you under handicap a boat, one boat suffers. If you over handicap a boat, the whole fleet suffers.”. Certainly, you could take your case to those Authorities or organisers if you feel at any time that those ‘foundation principles’ are being breached.

How can you trust orc when it fancy system, fails and they apply penalties to stop a boat winning, this an avuse.

I've got a bit of a twist to offer.  Appx J1.1(4) states ...

Here in the Chesapeake Bay, PHRF is controlled by PHRF of the Chesapeake and the PHRF-splits are predetermined. Therefore, a boat knows what PHRF-fleet they will be in at the time of entry.  I would argue that is a key piece of information in the "decision to race". 

Now, it is common for the NOR to state that fleets might be combined depending upon number of entries.  That is very common in the PHRF B/C fleets as those numbers have dwindled over the past 20 years.  Often an NOR will state this possibility. 

So, IMO, if an OA intends that the RC will make PHRF-splits on-the-fly that differ than the established region splits ... then the NOR should have a statement that says exactly that ... and give a time/date that this information will be posted so that a boat can decide whether or not to compete. In doing so, I would suggest a statement added to such an NOR, "This changes Appx J1.1(4)."

PS:  In other words ... it's a bit meaningless to state that PHRF A, B classes are invited to enter if the split between them or the rating-range they encompass is undefined or subject to last-min change.