Pinephone charging issues after fully depleting battery.

[Subsentient]

Some updates back, when my phone got run down to 0% charge, it appeared to not be charging,
  .......   then it was charging at .02 watts
for a long time..
 But when it got to a few percent charge it finally started charging properly again.
  I am not certain if that was hardware or software 
IT has went to 0% one time since,  but it seems to charge OK now.

The nature of working with Beta  operating systems 'I guess'  ?

That sounds normal. If the battery gets near completely flat, it will take a while of charging at a very low current to get it to a level it's safe to kick on the full charging current. There's a small hardware defect where the phone slowly drains battery when turned off, so if you're gonna store it, take out the battery first.