Yep. There are command line tools in the interface SDK download: https://www.silabs.com/products/development-tools/software/interface#software

AN721 has info on how to use them (section 4.1) : https://www.silabs.com/documents/public/application-notes/AN721.pdf

What OSes does this happen on? Win7? I see a very old case in our ticket system where Windows 7 machines were failing to print with Okidata printers on USB 3 ports. Win 10 didn't have an issue. The problem ended up being that Windows 7 does not support USB3.0 natively, so the drivers for the 3.0 hubs have to be supplied by the hub makers, and those can be unreliable.

Maybe that's the same thing here? If so, I would first try making sure that you have the latest USB3 hub drivers installed, from whomever makes the computer's USB3 hub chips.

I've seen this behavior on our 8-bit devices when they have a poor amount of decoupling capacitance on the supply rails, perhaps the same applies to these?
 

AN0002 (https://www.silabs.com/documents/public/application-notes/an0002.0-efm32-ezr32-series-0-hardware-design-considerations.pdf) recommends 0.1 uF at each supply pin (including VDDREG), and another 10 uF on each supply rail (IOVDD / AVDD/ VDDREG)... how is your capacitance on these pins / rails? are the 0.1 uF's close to the pins they're decoupling?

<Line 39, app_bumode.c>

// Turn on RTCC clocks so we can read from its registers
CMU_ClockEnable(cmuClock_CORELE, true);
CMU_ClockSelectSet(cmuClock_LFE, cmuSelect_LFXO); // <-- insert this line
CMU_ClockEnable(cmuClock_RTCC, true);

In the legacy 8-bit MCU IDE, there is an option to upload the contents of the memory to a text file. This can be useful to record the firmware image on a device:

However, the format that is produced is non-standard - every byte of flash is recorded in text, separated with a new line, e.g.:

00
00
82
20
81
02
41
03
00
80
00
20
c0
02
40
09
00
00
02
20
80
00
00
02
02
80
12
...
etc.

It may be useful to convert this format into a binary format. Attached to this case is an executable, as well as its python script source, that performs this function. The usage for this executable is:
 

MemoryUpload2Bin.exe -m <path to memory upload txt> -b <path to binary to be created>

Binary files can be generated from several toolsets, or even by uploading the memory contents of a device using Simplicity Studio. However, it may be useful to convert these .bin files into a .hex file. An executable, as well as its python script source, has been attached to this article to perform this task.

The usage of this file is:

Bin2Hex.exe -b <path to binary file> -o <path to hex to be created>