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SS1 and SS2 are not supposed to work together. Nor is SS2 supposed to replace SS1 on an existing save. If you switch to ss2 do so on a fresh save. I don't think you are going to have much luck finding solutions for any issues arising from switching from one mod to another as it's just not what you're supposed to do. Good luck though.
On a sidenote: even if everything seems to work fine now, you're asking for trouble big time. If I were you I'd switch back to ss1 and reload a save from before your switch to ss2
Thanks for the answer, anyway I have played many hours after the "switch" and it is really working well, the only issue is the happiness value shown on HUD that does not change. The plots are even upgrading normally. Anyway, if someone can help me to fix the happiness issue is good, otherwise i can live with it.
Happiness stuck is a known issue and thus far never been resolved. The only thing we have done to resolve it is fresh start. Alternatively if you have a mod that can tell you settlement TARGET happiness then you one could manually adjust the happiness level with some console commands to match the intended level. This of course does not compensate for fluctuation and isnt really a solution.
BTW this is most likely not the result of switching from SS1 to SS2, as I had this issue on the fresh start once.