Processing a lot of $wpdb isn't insert all the data

In my plugin the user provides some CSV files that are processed and either inserted or updated based on a sku (which acts as a foreign key to my DB and a primary key for where the CSV comes from).

I process each line and either insert product info or updated based on if the sku is available. There are 5503 products total. I have two tables one to hold the product id and sku and another to hold the details for that product.

when I run my function I check to see if the sku has a match. If not, I insert into the tables, if it does, I update. The first time I run, obviously everything should be an insert. I’ve done some debugging and found that insert is run every time, meaning there’s not an error causing updated to run.

I’ve ran print_r on the prod_details insert and I get all 5503 sets of arrays so nothing is being skipped. The products table is correct but for some reason the prod_details table doesn’t get all the inserts, only about 4122 are inserted of the 5503. I’m not sure if I’m dealing with a timeout, maybe a synchronous issue.

I’ve compared the skus between the two tables and found large chunks missing.

$prodTable = $wpdb->prefix.'products';
$prodDetails = $wpdb->prefix.'prod_details';

$skuId = $wpdb->get_var("SELECT id FROM $prodTable WHERE sku=$sku");

if($skuId) {
    //update the product table
    $wpdb->update(
    $prodTable,
    array(
        'status' => $status
    ),
    array(
        'id' => $skuId
    )
    );

    $wpdb->update(
    $prodDetails,
    array(
        'prodName' => $prodName,
        'typeName' => $prodType,
        'siteTypeName' => $siteType,
        'subTypeName' => $prodSubtype,
        'prodProducer' => $prodProducer,
        'styleName' => $prodStyle,
        'supplierName' => $supplier,
        'prodVintage' => $prodVintage
    ),
    array(
        'sku' => $sku
    )
    );

} else {
    $wpdb->insert(
    $prodTable,
    array(
        'sku' => $sku,
        'status' => $status
    )
    );
    $wpdb->insert(
    $prodDetails,
    array(
        'sku' => $sku,
        'prodName' => $prodName,
        'typeName' => $prodType,
        'siteTypeName' => $siteType,
        'subTypeName' => $prodSubtype,
        'prodProducer' => $prodProducer,
        'styleName' => $prodStyle,
        'supplierName' => $supplier,
        'prodVintage' => $prodVintage
    )
    );
}

I understand there’s some normalization I could probably do here but that would explain the insert issue. The above loops for each line of the CSV file (5503 times).

My local database inserts everything fine.