For me it sounds like you are just having the known issues which have persisted for many of us since 10.3.0 where endpoint devices (e.g. Ikea, Sonoff or Tuya sensors) just randomly drop out of the network. I’m still having those issues on 10.3.2 and I’m not sure when/if Athom will fix them.
Personally I spun up zigbee2mqtt on my NAS with the channel set to 25 which for now only hosts my sensors and this has been rock solid now for a week (before they dropped out daily), so I’m very certain that it’s Homeys fault.
EDIT: Just saw that they released 10.3.3 which has this disclaimer text at the bottom:
Homey Pro (Early 2023) Changelog | Homey
Note: there is currently an issue related to Zigbee in this, and previous firmware versions. Some Zigbee end-devices may experience difficulties reconnecting to Homey Pro after a reboot or firmware update. Also, in some cases Zigbee might become unavailable due to this issue. We are working together with Silicon Labs to resolve this issue as soon as possible. We understand the frustration this may cause and apologize for any inconvenience it may bring to your smart home experience.