Remember that the purpose of the RS throughline is to illustrate the emotional experience of grappling with the problem at hand. Thus, it’s not necessarily an issue that the RS dynamic feels different during different parts of a story. It should feel different, especially from act to act, as the problem does (or doesn’t) get resolved.
Think about the role that Elizabeth and Darcy’s relationship plays throughout P&P. The overall plot is about the Bennet sisters finding husbands, and the heart of the story consists of one of those sisters and her husband-to-be negotiating the rocky emotional road to mutual affection and love. And how boring would P&P be if the dynamic between Lizzie and Darcy never shifted? The book wouldn’t be worth reading.
On the other hand, there’s a reason why most stories keep the RS between the same two characters from start to finish. It’s a lot harder to build a cohesive arc if you start swapping out the players partway-through. It certainly can be done, but it requires a deft touch.
In stories that employ this strategy, the focal point will switch from one relationship pairing to another in sequence, minimizing overlap (and thus redundancies). Trying to have three “stacked” RS pairings operating simultaneously throughout the story would result in either a lot of dead weight, wherein the same emotional material gets “chewed” and then chewed again (and again!), or in a chaotic, overwhelming mess.
This is why stories that use this technique will almost always place more emphasis on one of the RS pairings than the other(s), starting and ending the story with it and generally giving it more time and attention. As Jim alluded to in the How to Train Your Dragon example you provided above, the Hiccup-Stoick pairing is the primary one, and the other pairings serve as “pinch-hitters” for parts of the story where the plot requires one of the central players to be temporarily absent (like, say, the section where Stoick sets off on a journey with his fleet to locate the dragons’ nest, leaving Hiccup behind).
Stories like this will do their best to “tie” these RS pairings together through other means, so that each leads to the next as organically as possible. Think of Stoick putting his son in a dragon-fighting class while he’s away-- thus bringing Hiccup into close proximity with another member of the class, Astrid, who will temporarily take Stoick’s place in the RS throughline.
What concerns me about your story, Dido, is that the first RS partner (the sister) seems, at a glance, like a much more significant figure in your MC’s life than the second (their employer), even though the dynamic with the employer clearly gets the bulk of the RS runtime. Remember, readers will tend to latch on hardest to the first RS pairing you give them, assuming, quite naturally, that it will prove the most important (why else would you be placing it front-and-center?). As a result, they may feel betrayed if one of its constituent players dies at the end of the first act, especially if the character who comes in to replace them seems to play a less significant role in your MC’s emotional life.
In other words, readers may accept a permanent mid-story pivot from one RS pairing to a second more-impactful one if the switch elevates the stakes-- say, by shifting the focus from an MC’s relationship with their coworker to the MC’s relationship with their child. Shifting in the opposite direction is usually a bad idea.
This is all to say that in your story, I’d recommend either starting with a less important RS pairing than the primary one you intend to give the bulk of your attention to, or finding a way to start the story with the primary pairing, even if only for a few scenes, before temporarily cutting to a second one, if that’s what the plot demands.
