MKR1000 Battery Charging Question

The documents recommend a 1400-1500mah battery for the mkr1000, based upon a standby charge time of four hours @ 350mah. Does that mean that the mkr1000 would only charge an empty 3000mah battery for four hours, up to roughly half capacity? What exactly does the standby charge time mean? Thanks.

The best way to get detailed information on the charging system is from the datasheet for the MCP73830 charge management controller IC used by the MKR1000 (as shown in the MKR1000 schematic):
The charge current of the MCP73830 is set via a resistor connected to the PROG pin. In the MKR1000 schematic, you can see that the resistor used is 2.87 kOhms (2K87). In section 5.4 of the datasheet, the equation is given IREG = 1000 / RPROG. This means that the charge current is programmed to 1000 / 2.87 = 348 mA, which matches the 350 mentioned in the documentation.

In section 5.4.1 of the datasheet, it says this:

If the internal 4-hour timer expires before the recharge
voltage threshold is reached, a timer fault is indicated
and the charge cycle terminates. The MCP73830/L
devices remain in this condition until the battery is
reinserted, or the input power or CE is cycled

So I think that your interpretation is correct.

Is there a way to eventually cycle the CE pin on the MCP73830 to continue charging a battery?

The CE pin is not connected to the microcontroller on the MKR1000, so you can’t do it without modifications to the board. The schematic does indicate that pin is broken out to a test point (TP2) on the board, which should make the project easier if you do want to connect a wire from the CE pin to a pin on the microcontroller.

Just beware that the safety timer is there for a reason and you need to be very careful with lithium batteries so they don’t turn into fireballs.

The test point is circled in red in the picture:

Thanks for tracking this down! As you said, just because something is possible doesn't mean it's a good idea. I'll keep a fire extinguisher handy if I try anything crazy.