My memory topic video, greatly helps.
But, you would want to...
1. Uninstall ALL HMODS
2. Uninstall HAKCHI2
3. Delete TEMP folder from Hakchi2 Directory
4. Flash Custom & Original Kernel
5. Flash Games (Try to stick to 275-300 Mb Range, and compensate for HMODS)
6. You can wipe all Saves on Mini by following my posted video on that, as well.
7. Reinstall HMODS. It is always best to install HMODS, after the GAMES. This will give you more space to work with from an initial clean state.
8. You do not necessarily HAVE to uninstall Hakchi2, unless you have a memory conflict. You can try skipping step 2, and doing the rest. And, if things do not pan out for you, then redo, following Step 2
I have cleaned up hundreds of times with this method, as well as helped many others. Lastly, I would suggest using the Debug version, as it gives you an excellent read on remaining memory, with each flash.
My YouTube Channel with Memory Clean Video...
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NES Classic - Pokemon Mini Test (Core posted in my Mega Thread Topic on Reddit)
https://www.reddit.com/r/nesclassicmods/comments/6j2zoo/the_mega_hmod_thread/
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9 out of 10 times, you can Flash Custom Kernel and be fine. It is mainly necessary to uninstall if you have a true conflict. I made another post, with a video link, instructions, etc...that should help you out
I have used this method over 1000 times via TeamViewer, with my own set-up, tests, etc. I also posted another Core in my set