Following is my idea off my head, so it may not work for you
but (I hope that) worth giving a try...
I wonder if updating firmware of the board may affect the situation.
Can you try PSoC Programmer, this tool is located in
C:\Program Files (x86)\Cypress\Programmer
on my System.
After starting PSoC Programmer
(1) select Utilities tap
(2) select Upgrade Firmware
If it goes well, quit PSoC Programmer and start PSoC Creator
and try to acquire the port explicitly.
I assume that you are using the main board of the Kit-059 (not the detachable kitprog). If you are using the USB, you can program the P5L with same connection. You need the USB pins + reset signal
If you use the USB in your application, the problem is you can't debug.
Note: pay attention that Kitprog working as mass storage doesn't support kit-059. I mean, as mass storage, kitprog can't program other P5LP (see KitProg User guide - www.cypress.com/file/157966/download - section 4.3, 1st question)
I'm very sorry but I could not read that much.
Recently I had a chance to program SWD/SWCLK pins to GPIO and re-acquired them from KitProg3, it was PSoC 4M though,
so I was hoping that re-initializing the KitProg might help, since you could at least leave the mass storage mode.
But apparently it was not a useful idea for this case.
I know that the KitProg doesn't support mass storage programming on the 059, which is why I want to turn it off...
Re programming via the USB pins: I am using USB, and one of the things on my to-do list is to figure out how to do OTA firmware upgrades. When you say it's programmable via the USB pins, you don't mean via the USB protocol, right? Instead I am connecting the programmer to the same pins that USB uses? Because I don't think that helps me much --- I still need to connect the programmer somehow, of course. If the board supported self-programming via USB without special firmware, that would be awesome.
Press the RST button and hold it for 30 sec and then unplug the USB cable and then Plug it in and try it again,
As stated above, I can't rely on the reset button being accessible and so need a solution which doesn't involve it.
You need the KitProg or miniprog, connecting SWD pins to USB lines and the reset line. I use the miniprog3 with the 5 pin connector.
But you need the reset always. (I did a special cable connecting the reset line to ID line in the connector - pin 4 - )
Of course, you don't use the USB protocol