I do not have experience to say one way or the other.
From what I have gathered on this website, I anticipate that seedlings do not flower normally anyways in their first few years until they settle down into a routine. But that is only from reading other people's comments. So, even 'naturally' flowering daylilies time of flowering is not to be trusted in the very early phase of growth. I could be 100% wrong, I am just going by what others have said about their own seedlings.
Given that your own breeding program is based on time-of-flowering, that is the most important component to you and I can totally see that it may be crazy to mess with that. Having said that, you do not know until you test it. Hypothesis is one thing, but hard data is always the goal to base things on. And without hard data, through testing and observing, we will never know the answer.
But I honestly doubt that the GA will have long-term effects. I expect that if it is used only in the first year to have a 'sneaky-peeky' at the flowers then the daylilies will settle into their normal flowering routine in the second year and beyond, just as they would have done without manipulation.
From what I have quickly just learned the GA works by releasing intracellular calcium to activate signaling pathways. It seems to be a very transient phenomenon. I would have been worried if the GA changed epigenetic factors permanently (e.g. re-writes DNA methylation), but it does not seem to. So the genetics of the plant remain the same as they have always been (and presumably the epigenetics also do). And as such natural future flowering should be driven by those same genetics that have not been altered in any way. I would have to read more to be sure, but the data probably already exists regarding crop biology (e.g. do they spray every year to keep getting more fruit, yearly, or do they only spray in year 1 and get more fruit forevermore). I would need to dig around, I think.
Edited to add: Actually, I just realized that even if you are correct and the GA changed flowering-time permanently this would be exactly what you want. Just spray any daylily you like at a late timepoint and it will fire out a very-late scape. If it keeps doing this yearly then your breeding program is all-set. All it took was a spray bottle, rather than complex hybridization crosses.
