This usually points to the messaging app/protocol on the phone side rather than a Windows 11 setting in Phone Link.
A reported resolution for this exact symptom was:
- Samsung Messages no longer worked correctly with Phone Link for that conversation view.
- Switching to Google Messages and turning off RCS restored replies back into the message thread instead of only appearing under Notifications.
Also check the core Phone Link connection items, because notification-only behavior can happen when message sync is partially working:
- On the Android phone, confirm Link to Windows is updated.
- In Android Settings > Apps or Apps & notifications > Link to Windows, make sure notifications are enabled.
- Make sure Do not disturb is Off.
- If battery optimization is enabled for Link to Windows, turn it off:
- Android Settings > Apps & notifications > App info > Link to Windows > Advanced > Battery > Manage Battery Usage > Battery optimization and set Link to Windows to Don't optimize
- or on some devices: Android Settings > Apps > Link to Windows > Battery > Optimize battery usage, choose All, find Link to Windows, and turn it Off.
- If the device used to work and now does not, unlink and reconnect:
- On Android: Link to Windows > Linked Account > Account Settings > Sign out and unlink account
- On PC: Phone Link > Settings > Devices > Add new device
If the issue is only affecting some conversations, the strongest match is the Samsung Messages/RCS behavior. Using Google Messages with RCS turned off is the documented workaround from the matching case.