[R] RTools and previous Cygwin installation--conflict?

[Brent]

Background:
    --I already had the latest 64 bit cygwin (1.7.28) installed on my Windows 7 box
    --I am a new R user; I just installed the latest 64 bit R today (3.0.3)
    --a coworker told me that I also need to install RTools, so, I also installed the latest RTools (3.1) from
        http://cran.r-project.org/bin/windows/Rtools/
    --during RTools installation, I accepted all the defaults, including "Cygwin DLLs"
    --the sole additional item is that I checked to modify my PATH system env var

~~~~~~~~~~

So what's my concern?  That modifed PATH system env var.  After installation, PATH looks like
    c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;...;<my cygwin 64 bit path>
So the RTools stuff is before my original cygwin path.

This choice means that RTools should work just fine.

***But will it screw up my normal cygwin sessions?***

In particular, if during a cygwin session a command is needed and a command with that name is found in Rtools, I assume that that version will be used.  But it may not be the newer one expected by cygwin--could that cause problems?

Warren Young's very detailed answer here
    https://stackoverflow.com/questions/18329233/is-it-advisable-to-switch-from-cygwin-32bit-to-cygwin-64bit
indicates that 32 and 64 bit cygwin do not mix well...

~~~~~~~~~~

Some more info.

I accepted the installer's default to include "Cygwin DLLs", even tho I already had 64 bit cygwin installed, because of this note:

    "The Cygwin tools have been updated to versions current as of November 19, 2013. Cygwin now builds separate 32 bit and 64 bit versions; we include 32 bit versions of the tools. If your system only has 64 bit Cygwin DLLs installed, you will need to add our Cygwin DLLs to your path (or install the 32 bit Cygwin DLLs into Cygwin)."
    http://cran.r-project.org/bin/windows/Rtools/

But while web searching this issue, I came across a contrary recommendation:

    "Some of the R tools use the Cygwin DLLs, which are included.  If you already have Cygwin installed, you should not install these"
    http://cran.r-project.org/bin/windows/Rtools/Rtools.txt

(That last instruction, by the way, goes back many years, at least to 2008:
    http://www.r-bloggers.com/wp-content/uploads/2008/12/Rtools1.txt
)

So, which instruction should I follow?

~~~~~~~~~~

I apologize in advance if this issues has already been discussed before, but all attempts today to search this email list's archives at
    http://tolstoy.newcastle.edu.au/R/
always return 404 errors.

I found a 2008 discussion of this issue here
    http://www.r-bloggers.com/rtools-and-cygwin-on-ms-windows/
which suggests temporarily hacking your PATH when launching RTools.