When you replace a long inserter with lets say the long fast inserter it doesn't return a regular long inserter to your inventory it just deletes the item and places the new inserter.

Check your inventory to see if you get a regular yellow inserter instead. The default setting is when long inserters are picked back up (by either mining, bot, or fast-replace), they return the base inserter (which for a long, is a yellow). This is because the default setting also makes long inserters a shapeless recipe of their base inserter (as in you craft a long inserter using a yellow inserter and no other ingredients).

You can change this behavior in the settings, if you want the original crafting recipes, and permanency of long inserters.