I can't speak for Bese/Baselick at all, but I will briefly talk about the second part, and only in England from the Anglo-Saxon to Mediaeval period.

There are two types of things going on:

1. There are settlements of which we have no record. This is sort of cheating however, because the records are very thin on the ground in the AS period so it's hard to compare something if there's no prior record. We know settlements exist, because we dig them up during construction (and especially during the Victorian period with the railways), or metal detectorists accidentally find them. Part of the problem is then linking that to a place-name that we may or may not have. Sometimes we do have the placename, but no idea what it's referring to: Bede mentions numerous monasteries in Wales that we have no idea where they are, and the lack of contemporary maps is a problem (the first good maps come in the mid 1500s). Things survive generally by accident, and as the AS often built in wood, rather than stone, it makes things harder to find even if we do have a) a name and b) where it should be.

2. There are settlements which we have record of, but have disappeared (about 3000). Most of the time they never truly disappear (except maybe in the public eye) - we have records, so we often know where they should be, or we have archaeology to help us. They disappear for all sorts of reasons. My favourite is Dunwich, a thriving, major town in East Anglia, with a port, priory, friaries, 6 parish churches, 2 chapels, and a population of 3000. A storm in 1328 destroys part of the town and moves enough gravel into the harbour to block the port. Another storm 20 years later washes 400 houses into the sea, and another storm 20 years after that, destroyed most of what was left (I think I found the planning architect!) Sea changes altered other port-oriented towns around the coastline of Britain, meaning that they were now inland, and so they lost their importance. Climate change affected towns - Britain used to have wineries, but by 1400, they're pretty much all gone, taking any associated settlements with them if they cannot innovate (although often related to the Church). Some simply disappear- 26% of villages ending with the place-name of 'thorp' disappear in the East Midlands. Some were cleared by William the Conqueror's creation of the New Forest in Hampshire, the Northern parts of Britain succumbed to Scottish raiding in the 1300s, the French, regardless of their elderberry perfumes, caused a number of Southern coastal villages to be abandoned. The Black Death took many a medieval village, monks could kick out people so they could build their isolated settlements, enclosure took over villages during the 15th century, landlords could engross houses if they were feeling rambunctious, building parks could displace people in the later 18-19th centuries.

So it's quite common in England that things disappear, but they generally don't disappear out of history completely- we have hearth tax records, or bits in the Domesday book etc., to help us find them, and then we dig them up (sometimes). Why they disappear is due to a whole host of variegated reasons. The further back you go of course, the more complicated it becomes (try mapping charters to a modern map for example!) as we have fewer sources to work on.