For whatever it's worth, there was a time (Stormblood era) when the quasi-official dev. team answer to, "How do rejoinings make Zodiark stronger but Hydaelyn weaker?" was "That's a good question and we will come up with something." There were a lot of plot devices that - as I like to call it - "didn't have an exit strategy" at the time. The tidiness with which they were cleaned up varies from case to case.

For example, Elidibus (back in the days when his response to Lahabrea's death was little more than, "Well, that's annoying and inconvenient and more work for me.") said that being rejoined 7 times had resulted in the souls of the Source's becoming "weak and wan" (English) or "on the verge of inhuman" (Japanese) or "degraded and more spiritual" (French). In retrospect all of them should probably be ninja-edited to, "drawing ever-closer to regaining their true form" or whatever...but they remain for now.

Lines about Hydaelyn getting weaker as a result of rejoinings are from the same era. Another interesting facet of it is that Hydaelyn has been gifting crystals of Light to Her chosen before every Calamity and crystals that survive from previous eras show that they also get weaker each time.

Quote Originally Posted by Cleretic View Post
I forget who exactly told us 'every Calamity makes Hydaelyn weaker', but we should take into account the possibility that they just didn't have complete info.
Some were Hydaelyn Herself so we're stuck working around that. When Hydaelyn referred to Her increasing weakness, it was usually explicitly contrasted with Zodiark's increasing strength or having suffered a calamity so I think the other option is still pretty workable as an explanation.

Zodiark was consistently said to be stronger than Hydaelyn prior to and during their battle. The Unending Codex highlights that Zodiark was "unable to resist" after being fragmented, perhaps lending support to the "maybe she may have sundered Her energy but perhaps didn't create 14 copies of own Her soul/will" interpretation. And from the very start every act of direct intervention on Hydaelyn's part cost her dearly. Projecting a shield into the Praetorium put Her on life support. It's plausible that between empowering Her champions, trying to recover after / work around the Calamities, and being subjected to the increasing presence of Zodiark's Darkness, She suffered a net loss of available resources in spite of whatever the rejoinings gave back to Her.