I wanted to change some staves, making them one handed. Using the CS i changed some staves from "blunttwoclose" to "bluntonehanded". Now all the enchantments are missing from the staves in-game. After checking in the CS again, is shows the staves as not enchanted.
Why do the enchantments disappear and how can I avoid this?

Were the enchantments added by a mod?

It could be that your mod is "overriding" the other mod, thus removing the enchantments that mod added.

It sounds like you did everything right, so I don't know why else the enchantments would disappear.

Well, yes and no. I'm currently using the mod "Wizardly Staves", which adds scripts to all staves, giving you a defensive version of each one. Then I found the mod "Better Staves", which makes all staves one handed.

I checked on how to merge 2 mods and read somewhere that merging a mod that adds scripts, usually messes them up and I wanted some staves, such as the steel staff, which looks more like a quarter staff than a mages staff, to still be used with both hands.

So I thought I'd just change them myself. I loaded the CS with "Wizardly Staves" set as the active file and changed the staves that I wanted.
The staves that lose their enchantment are not added by a mod, e.g. Wizard's Staff, Staff of Magnus, Staff of Hasedoki etc.
I first thought this was caused by changing a mod, but even after trying this without loading "Wizardly Staves" the staves still lose their enchantments.