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2 hours ago, Jim D. said:

 

Are you sure the separated layer isn't butter?  If it is, I used to encounter this issue often.  Then I learned on eGullet about the necessity of emulsifying the caramel and the butter--mixing water and fat, much like a ganache.  Now I add the butter soon after the caramel is removed from the heat and use an immersion blender to beat it in.  I haven't had separation since I started doing that.  You will need a sturdy immersion blender for the emulsification.  There shouldn't be a problem with reheating caramel and adding salt.  Perhaps you didn't get it hot enough to melt the salt?  I myself don't mind a little salty crunch in the caramel, especially if it's a nice-tasting sea salt. 

It couldn't have been butter because I didn't add any, but it could have been fat from the cream?

I added sugar and a bit of water, melted and heated to dark amber colour, took it off the heat and poured about 1/2 of the room temp cream in, stirred well and added the rest when the bubbling slowed down, stirred and transferred until cooled. And it was all good until I heated it back up today - the separation surprised me after coming back to check on it to see if it has cooled down -.-

2 hours ago, Jim D. said:

I used to encounter this issue often.

I've read the whole story, in the thread I linked to, about your pineapple puree endeavors. 

I didn't know this was even a thing. Every recipe/video I've seen on making caramel made it seem so easy - and I was so pleased when I managed to actually make it. A few days later I thought I'd add in salt and bam I learned something new - that separation could happen. But I'm still not sure I understand what caused it in mine, since it was homogenous before reheating.

2 hours ago, Jim D. said:

Now I add the butter soon after the caramel is removed from the heat and use an immersion blender to beat it in.

Do you blend while it's still hot?

Have you ever tried it after the separation already occurred? I wonder if it would work if you heat it back up and blend.

Edit: After getting back to the comment on salvaging separated caramel (from pastrygirl) I see this is exactly what pastrygirl alredy suggested - using an immersion blender after bringing back to boil (it must have clung to my memory in the background x)) but just slipped my mind when writing this comment.

I didn't use an immersion blender after boiling because I had such little amount of caramel it wouldn't even have been possible.

In the end I did as @pastrygirl suggested in the linked post. I added water and brought it back up to boiling.

That did help so thanks pastrygirl

A veery thin layer on top remained after cooling down - not even layer as much as some droplets but it fixed it to the point I'm ok with it. I didn't know further cooking would darken the color also - I thought that only happens when there's so little water in the caramel that it reaches way higher temperatures..

Oh, I think the salt has dissolved nicely when boiling for a minute too. I might not mind the grains of salt that much also, I just wanted to get it all melted since that was my plan so I guess it was a matter of stubbornness