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

Hello everyone

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.

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.

Matej

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