As of Jetpack CRM v.5.0.0, custom fields created in the Checkout Field Editor (Checkout Manager) for WooCommerce plugin can be synced with Jetpack CRM WooSync. To ensure it will sync properly, follow the guide below on setting up the custom fields.
Custom Fields in Jetpack CRM
Go to Jetpack CRM > CRM Settings > Custom Fields, and add your custom field. For example, Billing Test
. Then, under each custom field title, you will see a slug in teal, billing-test
in this example:

Custom Fields in Checkout Field Editor (Checkout Manager) for WooCommerce
Then, add the slug from the CRM Custom field to the “Name” part of the custom field in the Checkout Field Editor (Checkout Manager) plugin, using an underscore, so billing_test
for this example:

For more information on setting up and configuring custom fields in Checkout Field Editor (Checkout Manager) for WooCommerce extension, please check their guide here.
Note: Jetpack CRM custom fields follow the WP slug convention, thus the CRM custom fields use a hyphen in slugs.