Ok started several times over already trying to write this not to confusing.
First of you need to keep in mind the first beacon you place and fueled for the first time is straight away also your “home” beacon.
This persists until you manually assign a new beacon (area) as “home”.
Second beacons removed (by deleting or reclaiming) don’t exactly disappear from location until you delete them from your beacon list. Until then you can always track their location.
Third updating (the game does) takes a minute for beacons, plots, settlements and worlds.
These 3 are pretty important to keep in mind.
That said here are some options for you to try.
Grab a beacon and some fuel.
Go to an other settlement, place the beacon and fuel it.
(It should pop especially if you haven’t plotted there before. As i am guessing you started at that settlement.)
Having plot view (grid) on delete that beacon and wait until the plots refresh (You can see it on the plot grid). As it takes a bit of time till they sort them selfs out (you will see some stripes or so in squares for a few moments where your plots where). Make sure that all beacons are out of your list that used to be there.
[to finish this off]
I would do my first suggestion.
Just find a “new” settlement where you havent beaconed before. Like a portal hub or so.
It should trigger almost instantly.
I have beaconed and plotted a lot (since release). And remember something about the objective needing a “new” settlement where you haven’t beaconed before.
I hope this helps.