How to store strings into an array from a foreach loop?

To start off, I've read the handful of questions here asking similar questions but nothing that I could take example of and implement properly into my code. I've got an array that hold a few thousand numbers, they're the names of a file in a directory. I need to run a MySQL Query that searches for those file names, but I need all the individual queries to be in another array.

Here's my code to grab the filenames:

$dir = "C:/Users/EyeCandy-Brian/Desktop/jobs";

$files = array_diff(scandir($dir), array('..', '.'));

function truncate(&$fcn) {
     $fcn = substr($fcn, 0, 6); // The original is '100100.dat', I only need the number
};

array_walk($files, "truncate");

The array looks like this:

2 => string '100100'
3 => string '100101'
4 => string '100102'
5 => string '100103'
// About 1,500+ Total

And here's my foreach loop with my declared variables:

$limit = 0; // This is for testing, stops after 5 iterations.
$qryArrNum = 2; // The index for the $files array, [0] & [1] were '.' & '..'
$count = 0; // Which index I want to store the string in, starting at [0]

$qry = array(); // I declare $qry as an array

foreach ($files as &$qry) {
    $qry[$count++] = "SELECT * FROM `table` WHERE `sku` LIKE '%$files[$qryArrNum]%'";
    ++$qryArrNum;
    if (++$limit == 5) {
        break;
    };
};

Here's where it gets wild. When using var_dump($qry); I get '1001S4' which shouldn't be. Running var_dump($files); The first five strings of the array are:

2 => string 'S00100'
3 => string '1S0101'
4 => string '10S102'
5 => string '100S03'
6 => string '1001S4'

Then following that are the expected strings from the filenames:

7 => string '100105'
8 => string '100106'
9 => string '100107'
// On for 1,500+ again

So my question is, how do I get $qry to be an array that contains a string, each string being the MySQL Query containing a search for the first value from $files, and the next string in the $qry array will search for the next value from $files. Also, why are the first handful values in $files completely different than what's expected?

NOTE: I understand that running a thousand plus MySQL Queries sequentially will murder my server, I'll use implode(); to combine them into one large query, I just need to figure this out initially.