Before using Beltlayer, I used another mod, UndergroundPlus (https://mods.factorio.com/mod/UndergroundsPlus). In-game, I replaced all UndergroundPlus belts with Beltlayer belts. I then disabled UndergroundPlus. When the game restarted, it showed dozens of warnings about missing assets, including Beltlayer assets. Upon viewing the map itself, all Beltlayer entrances and exits were missing.

Beltlayer creates a connector for each underground belt in the game, to support different belt speeds. So you need to use the Beltlayer connector that corresponds to the default vanilla underground belts, instead of the connector based on a modded underground if you want them to survive that mod getting removed.