The usual cause is exceeding the ludicrously low limit imposed on the number of keywords in the building menus. Installing even a single mod that adds things to be built can take you over the limit. It doesn't remove the items (so ones you've already built will remain). You aren't given any error message of any kind. Items just disappear from the building menus.
It's a bad farce, but it's what we're stuck with because Bethesda made it that way for some unknown reason.
If that is the cause, the your only option is to mod the mods to reduce the number of keywords by splodging different things into the same menu. In some cases, this has been done by mod authors providing different versions of the mods or by mods that alter the menus. For example, I use the Wasteland Workshop Independent Patch mod, which creates a new entry in the bottom line of the building menu and moves the WW stuff into that (with appropriate submenus). There are keywords mods for settlements and armour and weapons that aim to have all mods using the same keywords in order to reduce the overall number of keywords, but they add a relatively large number of keywords so unless every mod you use is wholly compatible with them they'll make the problem worse.
I have no idea why Bethesda set the limit so low and hasn't increased it.
