In my testing while not always needed, this is good to do in case your switch won't boot into its emuMMC, steps below can be used to set the archive bits. Also good to run if you're getting corrupted game issues, especially if you use a mac.
Step 1. Inject hekate_ctcaer_X.X.X.bin to your switch (where X.X.X is the release version of Hekate.)
Step 2. Navigate to Tools.
Step 3. Navigate to Archive bit - AutoRCM.
Step 4. Tap on both options under Misc relating to archive bit. This can take awhile (especially if you have Retroarch).
Note: On hekate 5.2.0 and higher, there's only one archive bit option, just run that.