No worries!
Both structures will remain (even if they are a little too close, although I'm not 100% sure how you managed to pull that off ) and in terms of upgrades the one that is closer (down to the last meter) will be chosen; failing that, the one that was built earlier, although this sorting logic is easy to adjust.
However, I do remember promising an individual upgrade button (the mini-flag) for each utility structure to allow choosing which one to upgrade and it is still in my task list.
It has been delayed due to some internal complications surrounding the utility structures (it is trickier than it should be), but I still intend to implement this eventually.