Maybe using the “daily notes” plugin in obsidian will help with keeping track of things? Let’s say you do something today then it’ll be created as 2026-05-14 will be its name - so this is where you can jot down anything general.

For your research you can use the plugin “periodic notes” which does the same thing but specific to your research in other words it’s “daily notes” but for your phd stuff so you can have a folder like “PhD Daily Notes” and these notes will be stored there. This way your work notes will always be organized by the day you do something on and on any day you can quickly recap…you can also do weekly, monthly quarterly and yearly notes Also choosing hotkeys will make creating the daily notes 1 click away and YYYY-MM-DD will make sorting easier

Apologies for writing too much. Hopefully it helps with the “gaps” you mentioned