You appear to be bogged down matching all sorts of things that you're not interested in. You only want to match the "00001" in "XYZ12345_X05_20110805_9999999_00001.TXT". This regex does that:

/(?<=_)00001(?=[.]\w+$)/
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Then, you want to replace that with a random number. Your sprintf format indicates: seven digits, right-aligned, zero-padded. As the "%d" in the sprintf format already indicates an integer, you don't need to use int. Assuming zero is not a valid random number for your requirements, the range is "0000001" to "9999999". You can get that range with:

rand(9999999)+1
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So, putting all that together, we get:

s/(?<=_)00001(?=[.]\w+$)/sprintf "%07d" => rand(9999999)+1/e
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[Note: your "int( rand(100000)) + 999999" will produce this range: "0999999" to "1099998". I'm guessing that's not really what you want; however, if you want some different from the range I suggested, see rand for the values it returns and adjust accordingly.]

I ran some tests (which included edge cases) with this code:

$ perl -Mstrict -Mwarnings -le '
    my @test_filenames = qw{
        XYZ12345_X05_20110805_9999999_00000.TXT
        XYZ12345_X05_20110805_9999999_00001.TXT
        XYZ12345_X05_20110805_9999999_00002.TXT
        XYZ12345_X05_20110805_9999999_00001x.TXT
        XYZ12345_X05_20110805_00001_00001.TXT
        XYZ12345_X05_20110805_00001_00001xxx.TXT
    };

    for (@test_filenames) {
        s/(?<=_)00001(?=[.]\w+$)/sprintf "%07d" => rand(9999999)+1/e;
        print;
    }
'
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Here's one sample output:

XYZ12345_X05_20110805_9999999_00000.TXT
XYZ12345_X05_20110805_9999999_1656320.TXT
XYZ12345_X05_20110805_9999999_00002.TXT
XYZ12345_X05_20110805_9999999_00001x.TXT
XYZ12345_X05_20110805_00001_0901076.TXT
XYZ12345_X05_20110805_00001_00001xxx.TXT
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