At the very first I'd check the addon's comment section and FAQ, addon description of the addon.
Some addons got a first sticky comment with instructions what to do and check.
Follow these, and the FAQ/addon description.
As 2nd I'd check if the addon's needed libraries/dependencies are up2date to the newest versions.
Install and update them eacht time before playing to make sure they are updated and working.
It's the same like installing the addons. Only updating the addons, but fogetting the dependencies, might run you into such trouble!
If you are sure the addons and librraies are all up2date to their newest version, check if the ingame settings and addon versions in the ingame addon manager show the correct version numbers (compare them to the websites here).
And then you could check if you get any error messages uplon login, which might be the reason some addons break and refuse to work properly (not showing pins on maps but settings menus work e.g.).
At last:
Addons store theire settings, and thus your saved pins you have discovered, in the SavedVariables.
It's in the folder "SavedVariables", name <addonname>.lua where <addonname> is a placeholder for the folder name of the addon they belong to, e.g. HarvestMap.lua or similar.
Backup these files every week e.g. to be able to go back to these backups if you notice somehting not working as it should. Maybe it will save you the work to collect pins again.