Putty is not meant to be structural but a means to fill a gap or void to reduce movement. Builders who use it understand it's limited adhesion properties and place it in strategic locations that are either concealed or can be cover with trim. Hull flex is not usually any movement that would shatter cabin doors but does affect non structural areas with very slight movement. These movements at opposing surfaces will likely crack in sacrifice to surrounding structural surfaces. Cracking at the putty line is the usual and least detrimental result and normally occurs where it is not seen.
It's starting to sound like you want to believe or justify glassing over the helm joints between the cap and deck liner. I'm telling you I have done that with problematic results and learned why it didn't work the hard way. You may be lucky and never have an issue but I have broken things on my Potter hull out of shear abuse charging rough seas. It's why I am installing real bulkheads throughout the hull and tying it all together solid. Hopefully it will take more of a beating than I can now and then they can bury me in it. Good luck with your repairs. I've done a lot on my rig and got a lot of satisfaction from it but the learning curve on structural repairs is a steep one I will certainly never completely master.
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[b]The Moose is Loose !
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