Can anyone please have a look at this issue?
Why is the folder of project table 'file_path' used instead of the 'folder' information from the bug_file table? That would make a lot more sense to me.

function file_normalize_attachment_path( $p_diskfile, $p_project_id ) {
    // Check if the disk file exists at the given path
    if (file_exists($p_diskfile)) {
            return $p_diskfile;
    }

    // Retrieve the base name of the file
    $t_basename = basename($p_diskfile);

    // Priority 1: Retrieve the folder directly from the bug_file table
    $query = 'SELECT folder FROM {bug_file} WHERE diskfile = ' . db_param();
    $result = db_query($query, [$p_diskfile]);

    // Initialize the expected file path
    $t_expected_file_path = '';

    // Check if we have a result and use the folder path from the bug_file table
        if ($row = db_fetch_array($result)) {
                $t_path = $row['folder'];

                if (!is_blank($t_path)) {
                        $t_diskfile = file_path_combine($t_path, $t_basename);

                        if (file_exists($t_diskfile)) {
                                return $t_diskfile;
                        }

                        // If the file is not found, this becomes the expected path
                        $t_expected_file_path = $t_diskfile;
                }
        }

    // Priority 2: Check the project-specific path
    if ($p_project_id != ALL_PROJECTS) {
            $t_path = project_get_field($p_project_id, 'file_path');
            if (!is_blank($t_path)) {
                    $t_diskfile = file_path_combine($t_path, $t_basename);

                    // Debug Log: Check project path
                    error_log("Checking project path: $t_diskfile");

                    if (file_exists($t_diskfile)) {
                            return $t_diskfile;
                    }

                    // If we don't find the file, then this is the path we want to return.
                    $t_expected_file_path = $t_diskfile;
            }
    }

    // Priority 3: Check the default global upload folder
    $t_path = config_get_global('absolute_path_default_upload_folder');
    if (!is_blank($t_path)) {
            $t_diskfile = file_path_combine($t_path, $t_basename);

            // Debug Log: Check global upload path
            error_log("Checking global upload path: $t_diskfile");

            if (file_exists($t_diskfile)) {
                    return $t_diskfile;
            }

            // If the expected path not set to project directory, then set it to the default directory.
            if (is_blank($t_expected_file_path)) {
                    $t_expected_file_path = $t_diskfile;
            }
    }

    // If diskfile doesn't include a path, then use the expected filename.
    if ((strstr($p_diskfile, DIRECTORY_SEPARATOR) === false ||
            strstr($p_diskfile, '\\') === false) &&
            !is_blank($t_expected_file_path)) {
            return $t_expected_file_path;
    }

    // Otherwise, return as is.
    return $p_diskfile;
}

Why is the folder of project table 'file_path' used instead of the 'folder' information from the bug_file table? That would make a lot more sense to me.

According to 0009905:0020243 the folder field was meant to be removed at some point in the past. I guess it was assumed back then, that all attachments were expected to be stored in the same directory.

This does not make much sense to me, particularly in a context such as yours where the directory changes over time.

due to FTP limitations and for backup reasons its convenient to have them a little bit more organised then just all attachments in one folder. Over several years i get over 100.000 files.

can you test with 1 file?, keep same path as per previous server/config. work ok? "moving the file with FTP transfer".