Is it ok to replace or update Quartus's Cygwin installation?

Precisely 2 Question:

1. Is it Ok to replace delete Quartus's Cygwin installation and put a newly customized cygwin package in same default location?

location such as

C:\altera\13.1\quartus\bin\cygwin

C:\altera\13.1\quartus\bin64\cygwin

2. Is it Ok to use latest cygwin setup exe (from https://cygwin.com/setup-x86.exe) to update & install some other tools on Quartus's Cygwin installation?

like targeting the installation locaton by:

setup-x86.exe -R "C:\altera\13.1\quartus\bin\cygwin" -l E:\cygwin_pack_forInstall\ -v -P wget,chere,mintty,lynx

"Is it OK" means... will it cause error / weird symptoms in Quartus/NiosII/Qsys during build or the built binary-outcome?

Don't know has anybody had any study in such methods? :S

My scenario is, me & my colleagues all installed Quartus 13.1(windows version)

We might use NiosII shell to modify/enhance some workflow, this may need install/update some additional packages on cygwin

But i don't want to open another cygwin shell / install another cygwin installation to accomplish such enhancement. :S

And precisely one of the problem now is I found the default installed mintty working weird. (need press twice close button to close)

But if I update mintty, the problem is gone!