Pinning & the ignore list
Two tools keep the chain stable and uncluttered.
Pinning
When a connection is deleted, the app tidies up after it: if a system is left with no connections at all, it's removed automatically so dead-end nodes don't linger. Pinning a system switches that off — a pinned system stays on the map even when nothing connects to it any more.
Pin your home, your staging, and any system you want to keep regardless of what happens to the chain around it.
The ignore list
Add a system to the map's ignore list and mapping as you fly will never add it. This is ideal for systems you pass through constantly but don't want cluttering the chain — trade hubs and common waypoints. Remove it from the list later and it can be mapped again.
Together, pinning and the ignore list let you decide exactly what belongs on the map: keep what matters, and keep the noise out.