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I do much the same.
I bump up the windows partition to somewhere around 40Gbs and install all my programs, games and such on the same partition. A bit allotted for whatever Linux install I'm currently infatuated with and the rest for the storage of my personal stuff (typically on a whole separate drive, if I have my druthers...)
I don't really see the need for a distinct swap partition, but that's just me. If you want to keep the setup, I think resetting the boot flag might work, however, if it were me, I'd just wipe it all out and start from scratch since dealing with partitions from inside windows is just...well, horrible in almost every sense of the word.
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