Resizing Images Originally created in InDesign

I created a Logo in InDesign CS 5.5. It contains a number of different elements and I grouped all of the lements together. The original size of the Logo is approximately 15.5 X 7.5. I also formatted the interior of a book in InDesign. I copied and pasted the logo on the title page of the book, and resized the logo to around 6.75 X 3.25 by changing the percentage of the image. I am unable to change the width and height directly because it gives me a “Requested Value is not a Legal Dimension” message. After sending the interior to the printer for review, they replied indicating that the image was less than 300 DPI. Is there a way to manage or control the resolution of images originally created in InDesign so that when they are resized, the DPI will still be a desired resolution for print?

Thanks to all who replied.
If I understand correctly, I can control how my effects are rasterized by modifying the Transparency Flattener Presets, which is located in InDesign CS5.5 under "Edit" at the top of the screen. There is already an option for HIgh Resolution and it will Rasterize Line Art and Text Resolution to 1200 ppi and Gradeint and Mesh Resolution to 300 ppi. In addition, I think the Medium Resolution would work for me because it will rasterize Line Art and Text Resolution to 300 ppi.
Furthermore, in order for those effects to take effect, I understand that when exporting to a print PDF, I need to export with the compatibility as Acrobat 4 (PDF 1.3) in order to be able to modify the Transparency Flattener to Medium or High Resolution.
On the other hand, since I was exporting to a print PDF wiht the compatibility as Acrobat 5 or higher, I assume that it was doing this at the Low resolution, which was 288 ppi, which is the exact resolution that the printer cited. It is my understanding that if you create images with effects applied like Bevel and emboss, drop shadow, etc., and exporting them to a print pdf, it would be best to export as Acrobat 4 (PDF 1.3) in order to control the Transparency Flattener Presets.
Th

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I don't know anything about the jpeg encoders, but I do see code that doesn't make any sense to me:
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Image temp = new ImageIcon(resizedImage).getImage();What is the point of creating an ImageIcon from a null image?
int newWidth = (int)this.targetWidth;I don't see where you actually use this variable, so how does the image get resized?
For more help create a [url http://sscce.org]SSCCE, that demonstrates the incorrect behaviour and maybe someone will take a look at it.

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