I've recently been working with Xenon462, who wants to use this design with a stack of 2 supercapacitors. It got me thinking about how to overcome the problem of insuring that the voltage on SCAP is below 2.5V before shutting down the LTC4041 by yanking on the BSTEN_ and CHGEN_ pins. I came up with this possible solution:
The changes to the previous design (the UPS4041-LG4) are the substitution of the PIC10F202 with a PIC10F322 and the addition of R18 and M2. The PIC10F322 has an internal 8-bit ADC that is assigned to RA2/AN2 to monitor the voltage at SCAP. R18 and M2 switch the SCAP voltage to the PIC to prevent unwanted current drain from the supercapacitor stack when there is no power applied.
The PIC code will be modified so that the RA1 output won't be asserted until the shutdown period has expired and the voltage at RA2 is below 2.5V. This will insure that the LTC4041 wont restart the booster when the voltage at BSTEN_ and CHGEN_ fall below their 1.4V threshold, unless there is input power present.
[Edit 2019-11-17: Added C11 as insurance.]
A side benefit to this design is that it will revert back to the UPS4041-LG4 design by depopulating R18 and M2, and substituting the PIC10F202 as U2 (it is pin-compatible.)
The changes to the PCB were straightforward and increased the size by about 0.075 inch in one dimension.
I'll be ordering new PCBs after completing the new PIC code.