1. Upgrade issues
For example, if I built a store today, will there be any impact when I reconcile the time into the future with the past?
Where it doesn't matter: The store is still there. It will not disappear because of going back in time. It's amazing how things don't change in a store. All your items, including Nook Miles Tickets and bells, will not change.
2. Residents and housing issues
For example, then the little animal will ask you where you have been so long when you travel to the future one month later. Some small animals that have a bad relationship may move out or tell you that they don't want to live anymore. The long-term crossing is risky, and going back to the past has no effect on small animals.
If you think time travel is too troublesome, Buy ACNH Bells to complete the tasks you missed is also an option.