SourceTree - files marked as "Missing" in Unstaged files section - cannot get rid of them

Question

I am a new user of SourceTree. I migrated my HG repository to GIT repository and for easier version control I decided to use Sourcetree. Everything is working as intended, the only thing I am struggling with are files marked as "Missing" in unstaged files section.

My problem is with character encoding. Some files marked as missing have a black diamond with a question mark instead of our usual č, ž, š characters. Source tree interprets this as a new file that is missing instead of the original file which contains aforementioned characters. I tried everything, even creating a copy of existing files with that black diamond with a question mark or character code instead of č, ž and š. Nothing seems to work and I cannot get rid of these "Missing" files.

"git status" returns deleted state for all of the files.

"git reset" did not help.

Is there any other way to get rid of them because they are really bothersome to look at them forever. I am attaching image for clarity.

Thanks in advance.