There is a menu item:
Edit > Integration > Synchronize Integration
where you can tell Skyline that whenever you make a manual change to peak boundaries that should be applied to all or some of the other replicate.
There are also the menu items "Edit > Integration > Apply Peak To All" etc. which will apply peak boundaries to other replicates.
The "Apply Peak To All" menu item also works when you have multiple molecules selected in the Targets tree. If you have chosen the correct peak boundaries for all the molecules in one particular replicate, you could switch to that replicate, select everything in the Targets tree and then do "Edit > Integration > Apply Peak To All" to apply those peak boundaries to all replicates.
In Skyline 26.1 we introduced a new feature "Peak Boundary Imputation" which is supposed to solve some of the same problems that you are dealing with, but which works differently. There is a webinar here:
https://skyline.ms/project/home/software/Skyline/events/2025%20Webinars/Webinar%2027/begin.view
-- Nick