First, the web server you are using might not be running windows -- you should check on that.
Second, the location of the file is irrelevant to the webpage. You can put files all over the filesystem and all over the web. The code for the page itself has a reference to the location of the file. So this is transparent to the user as long as you put the files in the right place and refefence them correctly.
Third, the limit is on the PDA - not the PC -- it uses an old filesystem format, but if you are trying to keep them in sync then this is problem the crux of the matter.
Fourth, XP (and newer operating systems) have the following limits:
NTFS Size Limits
Files per volume
4,294,967,295
FAT32 Size Limits
Maximum number of files and subfolders within a single folder
65,534
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