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If you have to ask that question, then you should probably rework your application to use subdirs. Dealing with directories with that many files can waste a lot of resources.
The easiest way might be to create folders named 0 1 2 3 4 5 6 7 8 9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z and rewrite your script to seek/store the files in that manner.
But it really depends on your application and file naming scheme.
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