[Note]
This is  NOT  a "General Solution" for this kind error(s)
Rather, personal, first aid, bypass service to hide pop ups only
So, if it works for your case, Fine
OR, just go and find your own one, it is not for you.

.

This is quite annoying one, SDL should imporve this part somehow.

I have made a nice workaround. Ideas is so simple.
I have found that there are two Elements in sdlxliff file which realted with the error.
"reference" and "sdl:ref-files"
So, I deleted it (temporary).

Annoying message gone, Fine !!!

Now, you have finished your work, So you have to restore its "Pain in the neck Status" just like earlier.
-actually, You have to do it properly, for the next step of works.

Easy

I have made "Restore code" too.
Just OneClikc it.

Now, you are very happy.. right ?

Do Not Forget, AutoHotkey is an outsider, so you have to close SDL's document before you run AHK code. Or, it could be messed up.

Attached, Error Suppress code and Error Restore code
DFNF Suppress and Restore.zip

Enjoy