Changing the files permissions on Linux will not be a problem.
The new permissions that the file is given, when it is copied from the Windows machine, mostly depends how the file was copied (Samba, NFS, FTP, other). Most transfer programs try to replicate the previous permissions and apply to the new file; however, there are configuration settings for the transfer program that may change this behavior. This may either be in the form of a umask or other setting. The umask of the shell may also change the files permissions.