Development version, definitely unstable and insecure...

apply.php

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+<?php
+
+require_once('../../../init.php');
+require_once('functions.php');
+
+$currentUser = localAPI("GetAdminDetails");
+
+if ($currentUser["result"] == "success") {
+
+    $billables = array();
+    $prices = array();
+    $taxed = array();
+
+    foreach ($_POST["billable"] as $billableid) {
+        $billable = getBillable($billableid);
+        $billables[] = $billable->description;
+        $prices[] = $billable->amount;
+        $taxed[] = true;
+    }
+
+    print_r($billables);
+    print_r($prices);
+    print_r($taxed);
+
+    $result = localAPI("UpdateInvoice", array(
+        'invoiceid' => $_POST["invoiceid"],
+        'newitemdescription' => $billables,
+        'newitemamount' => $prices,
+        'newitemtaxed' => $taxed
+    ));
+
+    if (!$result["result"] == "success") {
+        die("Could not apply billables to invoice.");
+    }
+
+    foreach ($_POST["billable"] as $billableid) {
+        incrementBillableInvoices($billableid);
+    }
+
+    header("Location: /admin/invoices.php?action=edit&id=" . $_POST["invoiceid"]);
+
+} else {
+    die();
+}

functions.php

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+<?php
+
+use WHMCS\Database\Capsule;
+
+function getBillables($userid, $invoiced=false) {
+    $billables = Capsule::table('tblbillableitems')
+        ->where("userid", $userid);
+
+    if (!$invoiced) {
+        $billables = $billables->where("invoicecount", 0);
+    }
+
+    $billables = $billables->get();
+
+    return $billables;
+}
+
+function getBillable($billableid) {
+    $billables = Capsule::table('tblbillableitems')
+        ->where("id", $billableid)
+        ->get();
+
+    foreach ($billables as $billable) {
+            return $billable;
+    }
+}
+
+function incrementBillableInvoices($billableid) {
+    Capsule::table('tblbillableitems')
+        ->where("id", $billableid)
+        ->increment("invoicecount");
+}

hooks.php

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+<?php
+
+require_once("functions.php");
+
+add_hook('AdminInvoicesControlsOutput', 99, function($vars) {
+    $billables = getBillables($vars["userid"]);
+    print('<br><input type="button" value="Apply Billable Items" onclick="jQuery(\'#applyBillables\').modal(\'show\');" class="button btn btn-default">');
+    print('<div class="modal fade" id="applyBillables" tabindex="-1" role="dialog" aria-labelledby="applyBillablesLabel" aria-hidden="true" style="display: none;">
+    <form method="post" action="../modules/addons/whmcs_apply_billables/apply.php">
+        <input type="hidden" name="invoiceid" value="' . $vars["invoiceid"] . '" class="id-target">
+        <div class="modal-dialog">
+            <div class="modal-content panel panel-primary">
+                <div class="modal-header panel-heading">
+                    <button type="button" class="close" data-dismiss="modal">
+                        <span aria-hidden="true">×</span>
+                        <span class="sr-only">Close</span>
+                    </button>
+                    <h4 class="modal-title">Select Billable Items</h4>
+                </div>
+                <div class="modal-body panel-body">
+                <table>
+                <tr>
+                    <th></th>
+                    <th>ID</th>
+                    <th>Description</th>
+                    <th>Hours</th>
+                    <th>Amount</th>
+                </tr>
+');
+
+foreach ($billables as $billable) {
+    print('
+                    <tr>
+                        <td><input type="checkbox" name="billable[]" value="' . $billable->id . '"></td>
+                        <td>' . $billable->id . '</td>
+                        <td>' . $billable->description . '</td>
+                        <td>' . $billable->hours . '</td>
+                        <td>' . $billable->amount . '</td>
+                    </tr>
+    ');
+};
+
+print('
+            </table>
+
+                </div>
+                <div class="modal-footer panel-footer">
+                    <button type="button" id="doDeleteClient-cancel" class="btn btn-default" data-dismiss="modal">
+                        Cancel
+                    </button>
+                    <button type="submit" id="doDeleteClient-ok" class="btn btn-primary">
+                        OK
+                    </button>
+                </div>
+            </div>
+        </div>
+    </form>
+</div>');
+});

whmcs_apply_billables.php

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+<?php
+
+if (!defined("WHMCS")) {
+    die("This file cannot be accessed directly");
+}
+
+function whmcs_apply_billables_MetaData()
+{
+    return array(
+        'DisplayName' => 'Apply Billables to Invoices',
+        'APIVersion' => '1.1'
+    );
+}