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Now I'll add a few things, for OP as tips about those deposits and maybe how to cut into the mining. Thas is only if you already have the medium refinery (or the large one), so if not, push forward into base building missions.
Depending of the deposit, if you keep mine it, know there are way to expand some (if not a lot) of ressources without you needing to collect anymore, from cobalt, to copper (or whatever gives you chromatic metal from your planet), or other ways to get them (paraffinium)
So dig into refinery guides and tables... the time you spend to learn them will save you lot of ingame time to do what you like to do. Here are a few links from great work by some peeps (me not beeing the creator of those, so full credits to the ones who did those amazing works)
https://steamcommunity.com/sharedfiles/filedetails/?id=1456988316
https://nomanssky.gamepedia.com/Refiner#Medium_or_Large_Refiner
https://docs.google.com/spreadsheets/d/1m3D-ElN7ek3Y0f-1XDt0IW2l6HxfXi5n5Yr7VLwLbg4/htmlview?sle=true
Once you unlock Autonomous Mining Unit
https://nomanssky.gamepedia.com/Autonomous_Mining_Unit
Make use of them, they will get so much more minerals from the same deposit than you mining it.
So keep a few untouched deposits around your base... you'll thank me later...
Anyway, have fun playing the game ;-)
I found a (somewhat) fix:
1) Find deposit you want to mine.
2) Mine a little bit in the center.
3) Use flatten tool (middle click to switch to it) in a big circle well around the deposit.
4) repeat steps 2 and 3 until you reach the bottom of the deposit.
While this is a bit more tedious than just ravaging away with the circular mining tool, it doesn't leave anything behind and soothes my need for less empty deposits.
It is annoying to run or fly to so needed deposits to get there and see the hole from being minned already.
At those cases it could/should show some sort of tip like saying Visited or percentage or something else so we don´t waste time and resources going for nothing.
These spots also respawn eventually. The game only holds a certain number of terrain manipulations in memory. When you exceed that the oldest manipulation is cleared out of memory to make room for the new manipulation and the old terrain respawns. If that terrain was a resource node the node is back and can be mined again.
Alternatively get in your ship and glide over the spot. You can see deposits from the air and except for the silica only ones they are all shiny and easy to pick out if they are unmined. For most of them you can tell what mineral it is from the color and you can just keep flying until you find what you need.