Out of Stock Products Still Counted on Category Pages

After upgrading from WooCommerce 2.x to 3.x, I have a site that shows many blank pages in my shop categories. For example, there are 36 in-stock products of type X but the X category page shows 103 results and 9 pages, most of which are empty. The missing 67 products are out-of-stock and the pagination decreases when out-of-stock products are unpublished.

This problem is similar to the one described at https://github.com/woocommerce/woocommerce/issues/15455; however, get_term_by( 'name', 'outofstock', 'product_visibility' ) returns no result for me. I’ve tried disabling all plugins and reverting to the Twenty Seventeen theme to no avail.

I assume that the database changes for WooCommerce 3.x were botched on my install. Can anyone tell me how to fix the outofstock/product_visibility term problem?

Here is my status report:

### WordPress Environment ###

Home URL: https://blazingshuttles.com
Site URL: https://blazingshuttles.com
WC Version: 3.1.1
Log Directory Writable: ?
WP Version: 4.8.1
WP Multisite: –
WP Memory Limit: 256 MB
WP Debug Mode: –
WP Cron: ?
Language: en_US

### Server Environment ###

Server Info: Apache
PHP Version: 5.6.31
PHP Post Max Size: 8 MB
PHP Time Limit: 30
PHP Max Input Vars: 1000
cURL Version: 7.54.0
OpenSSL/1.0.2k

SUHOSIN Installed: –
Max Upload Size: 2 MB
Default Timezone is UTC: ?
fsockopen/cURL: ?
SoapClient: ?
DOMDocument: ?
GZip: ?
Multibyte String: ?
Remote Post: ?
Remote Get: ?

### Database ###

WC Database Version: 3.1.1
WC Database Prefix: wp_
woocommerce_sessions: ?
woocommerce_api_keys: ?
woocommerce_attribute_taxonomies: ?
woocommerce_downloadable_product_permissions: ?
woocommerce_order_items: ?
woocommerce_order_itemmeta: ?
woocommerce_tax_rates: ?
woocommerce_tax_rate_locations: ?
woocommerce_shipping_zones: ?
woocommerce_shipping_zone_locations: ?
woocommerce_shipping_zone_methods: ?
woocommerce_payment_tokens: ?
woocommerce_payment_tokenmeta: ?

### Security ###

Secure connection (HTTPS): ?Your store is not using HTTPS. Learn more about HTTPS and SSL Certificates.
Hide errors from visitors: ?

### Active Plugins (19) ###

Cloudflare: by John Wineman
Furkan Yilmaz
Junade Ali (Cloudflare Team) – 3.3.1

Contact Form 7: by Takayuki Miyoshi – 4.8.1
Facebook Widget: by Milap Patel – 4.2.1
Google Analyticator: by SumoMe – 6.5.4
Google XML Sitemaps: by Arne Brachhold – 4.0.9
Resize images before upload: by Simon @ WPsites – 1.8
Storefront Product Sharing: by WooThemes – 1.0.4
Storefront Sticky Add to Cart: by WooThemes – 1.1.6
The Events Calendar: by Modern Tribe
Inc. – 4.5.9

Woocommerce Advanced Bulk Edit: by George Iron – 4.0.4
WooCommerce Print Invoice & Delivery Note: by Triggvy Gunderson – 4.1.5
WooCommerce USPS Shipping: by WooCommerce – 4.4.8
Woocommerce USPS Label Printing: by wanderlust-webdesign.com – 2.0.0
WooCommerce: by Automattic – 3.1.1
WooSidebars: by WooThemes – 1.4.3
Wordfence Security: by Wordfence – 6.3.15
YITH Plugin Framework Temporary Fix: by YITHEMES – 1.0.0
YITH WooCommerce Gift Cards Premium: by YITHEMES – 1.6.9
NextGEN Gallery: by Imagely – 2.2.12

### Settings ###

API Enabled: ?
Force SSL: –
Currency: USD ($)
Currency Position: left
Thousand Separator: ,
Decimal Separator: .
Number of Decimals: 2
Taxonomies: Product Types: external (external)
gift-card (gift-card)
grouped (grouped)
simple (simple)
variable (variable)

Taxonomies: Product Visibility: exclude-from-catalog (exclude-from-catalog)
exclude-from-search (exclude-from-search)
featured (featured)
outofstock (outofstock)
rated-1 (rated-1)
rated-2 (rated-2)
rated-3 (rated-3)
rated-4 (rated-4)
rated-5 (rated-5)

### WC Pages ###

Shop base: #15 - /shop/
Cart: #16 - /cart/
Checkout: #17 - /checkout/
My account: #18 - /my-account/

### Theme ###

Name: Storefront
Version: 2.2.4
Author URL: https://woocommerce.com/
Child Theme: ? – If you are modifying WooCommerce on a parent theme that you did not build personally we recommend using a child theme. See: How to create a child theme
WooCommerce Support: ?

### Templates ###

Overrides: –