Deck sync/diff/dump ignoring --skip-ca-certificates flag deleting sni and certificates each time

# Issue

When running any command which supports the `--skip-ca-certificates` flag, console output shows `deleting sni` and `deleting certificate` which deletes certificates from the running Kong instance. If running ACME in Let's Encrypt's prod mode, this quickly depletes the quota (if you need to sync frequently).

# Desired outcome

When using the mentioned flag when syncing (or running other related commands), certificates and sni should not be touched (deleted or dumped to kong.yaml). I do not want to keep them stored in kong.yaml, so dumping them before syncing as a workaround is not an option.

# System info

OS: Ubuntu Server 22.04.1 LTS
Deck version: decK v1.19.1 (0d80472)
Kong gateway (Docker): kong/kong-gateway:3.2.2.0
Postgres (Docker): postgres:13
kong.yaml _format_version: "3.0"

# Reproduction

These are the steps (tried from scratch):
1. "Docker run postgres" (from documentation)
2. "Docker run kong/kong-gateway" (from documentation)
3. Install decK
4. Sync base kong.yaml (simple config with ACME plugin configured for the domain)
5. Trigger certificate creation (using ACME plugin - basic example from documentation with "kong" as storage)
6. Check validity of config and certificates by visiting my domain (with a service routed to mockbin.org)
7. Make any arbitrary change to kong.yaml (example: add https under protocols for a dummy service)
8. Run `deck sync --skip-ca-certificates -s config/kong.yaml`
9. The connection to the domain is no longer secure as certificates have been deleted

Other (tested) flags seem to work fine, however `--skip-ca-certificates` fails to work every single time. I've also inspected the test cases in this codebase, which seems to cover the flag, however I have not had the time to build and debug the project from scratch.

Start by running the reproduction with `deck sync --skip-ca-certificates -s config/kong.yaml` and inspect the existing test cases that cover the flag. Trace the sync, diff, and dump paths to find why certificates and SNI are treated as deletions or dumped despite the flag; done means those resources remain untouched while other configuration changes still apply.

Written by the indexing model from the issue text.