i need to synch some files between those two systems and windows is complaining about strange filenames eg : 菅野よう子 (Macross Plus - Original Sound Track I) - 03 - After, in the dark ~ Torch Song.mp3
Did you know some nice CLI tools for that ?
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I'm paraphrasing a bit from some other answers I found here. It appears that this can be a fairly difficult problem. However there are a couple of utilities that might help. The Linux utility detox appears to be mostly Unix focused but you may be able to adjust its settings using the RC file.
The main one discussed at linked StackExchange answer appears to have a German web-page so I can't vouch for it's usability or the safety of downloading from there (since I can't read German). However, I have no reason to distrust it.
Another answer suggested using pyRenamer which also has a GUI and may be more straightforward for starting out. You may also want to try to run the copy in a way that you can generate a list of files that are failing. I'd suggest a short bash script where you copy each file separately and check the exit code to see if the copy worked. This will give you the list of files you need to rename and save you a bit of time.
My final comment would be that it is highly likely you are running into the character limit. Windows can has a character limit for the length of each file but also for the overall length of the path. It should be fairly simple to rename your files to shorter filenames using the rename utility and find such as in the second answer linked above. Unfortunately, if you have a lot of files this may take a bit of effort.