Hyperlinking Between Multiple InDesign-Generated PDFs

Hi all. Here's my scenario:
Windows XP, InDesign CS3
We're working on a quarterly publication that contains an index. We want the index to be cumulative going forward. For example, the April 2008 issue will just have April 2008 articles listed in the index but the June 2008 issue will have April + June articles listed in the index.
We want to have the index listing link back to the respective articles. So I've figured out that in June I can:
1. Create the June index items using the InDesign index feature. This creates hyperlinks back to the articles (if we set up reference markers).
2. Open the April issue next to the June issue and copy and paste the April index over to the June file. This will copy the April hyperlinks over too but MAINTAINING their link to their April file.
3. Merge the two lists manually.
So then we export April and June to two separate PDFs. When I open the June PDF and click on a June article name in the Index, it hyperlinks to the June article. When I click on an April article name, it opens the April PDF and takes me to the respective April article. BUT... it closes the June PDF!
I don't want the June PDF to close... I want it to stay open so when I'm done with April's article, I can close the April PDF and the June PDF is waiting for me in the background.
I know that I can edit the carried-over April hyperlinks by hand in Acrobat to make them "open in a new window" - but is there any chance that there's a way (or a script or a default setting) to make all the hyperlinks to another PDF open in a new window without editing them all by hand in Acrobat?
I know this is a convoluted question so THANK YOU just for taking the time to read it over and think about it.
All suggestions are welcome.
Thanks!
-Jessie

Publisher can create CMYK files, you go save as, then choose PDF, then click on Options or something and change it to Commercial Press.  This is Microsoft's version of the Press Quality export setting in Indesign, with it converting all images to CMYK, downsampling to 300dpi etc.
NEVER EVER EVER USE THIS WAY TO CREATE PRINT FILES FROM PUBLISHER!!!!
Have I made myself clear? 
The CMYK images created this way have a terrible sort of under colour removal.  Think for example of a dark blue garment, where most of the garment is  something like 100C 60M 0Y 60K, but in the shadows it goes darker than  that, up to 100K.  Well in that area of 95 to 100% black in the image Publisher will convert it to only that, with no other colours underneath it.  But the areas surrounding it will be rich black.  This won't show up on digital proofs, even hi res ripped inkjets, and won't even show up on a press pass unless the machine has drying, because it is not until the ink dries off that you notice these weird photos....  Anyway what I do has already been said above.
1. Refry it first.
2. You should be able to sync your settings.
3. No, it just thinks it can.
In this case I actually had the Publisher files as well, so I printed them to PDF using Acrobat, and the images were fine.  Problem is the client had gotten used to text and other elements the way they looked using Publishers crappy CMYK export so I had to combine that with the proper images by cropping in Indesign..
Here's examples of what happens:
CMY channels only, BAD!
CMY channels only, GOOD!

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