If all your settings have been reset, it is because the browser decided to delete all Construct's local storage (sometimes confusingly called "cookies", even though Construct just uses this to remember your settings locally and doesn't send it to any servers or use it for tracking). Unfortunately that is beyond Construct's control. Browser settings, or browser extensions, orientated around privacy or tracking may be responsible for occasionally clearing data, so changing any related settings may help. You can also try pressing 'Request persistent storage' in the About dialog to request that the browser tries harder to keep your data (but AFAIK that's still not a guarantee).
If you were low on storage space I would guess the browser cleared storage to try to save space. The usual methods of clearing space on disk may help avoid that happening again, and Construct's 'Storage cleanup' dialog may help reduce how much storage Construct is using. It's also probably the case that the more storage Construct uses, the more likely the browser is to choose to delete its storage if the system is low on space.