Problem with long filenames in packaging processes

Hi,
I have a quick question regarding packaging processes of Thinapps. I'm sure others have the same issues too, but it is not much info on it on the interweb.
certain application have alot of subfolders in program files etc. when the developers made the application they did not go over the 255 NTFS filename limit. but when working with the virtual filesystem we get additional subfolders. This makes it difficult to move project folders etc.
Does any have some fix on this issue other than using subst command everytime for each folder?

We use Thinapp 5.1.
We already change the location but, but when storing the project folder on a share we cant avoid getting additional sub directories. The developers for all applications take this into account when they get the same problem in their development environments.
If Thinapp had not used ANSI codes that has a limit of 260 path length. then I dont think that it would an issue. Support case?
https://social.technet.microsoft.com/Forums/windowsserver/en-US/fbad33ee-b10b-4ab8-9370-a2af017ca46b/maximum-folders-in-a-folder-in-ntfs

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