The terminal listing may not include that attribute. There are lots of attributes which are usually not included (even in Opus).
The 7z format will preserve the attribute if told to. Tools creating or extracting files should really filter it out to avoid marking files as offline when they aren't, but it's easy to overlook. (We overlooked it ourselves at first as well.)
To fix the files, you can create a button in Opus to run the DOS attrib command on them:
Clear Offline attribute.dcf (266 Bytes)
That runs this command, in MS-DOS Batch Mode:
attrib -O {filepath$}
Select the files and run that on them and it should fix them.