The ISA3 Utilities are a set of software tools for the Silicon Labs Ember ISA3 Debug Adapter. With these tools you can manipulate adapter firmware as well as program chips in the EM35x and EM35xx family of parts. The latest downloads of these parts can be found here:

ISA3 Utilities

The latest installations of Simplicity Studio should also include the latest ISA3 Utilities in the subfolder:
 ~/developer/adapter_packs/em3xx/utils

For assistance using these utilities, please refer to this user guide:

UG107: ISA3 Utilites

Additional resources for the ISA3 as well as the EM35x dev kits are:

KBA: ISA3 connection troubleshooting steps

KBA: Connecting to ISA3 using Tera Term

TS6: EM35xx SOC Breakout Board Technical Specification

TS7: ISA3 Technical Specifications - READ SECTION 5 IF YOUR CANNOT CONNECT TO YOUR ISA3

TS8: EM35x Module Technical Specifications

TS9: EM35xx NCP Breakout Board Technical Specification 

UG110:  EM35x Development Kit User Guide (this guide has some example ISA3 setup routines in section 6 and 7)

AN717: Programming Options for the EMber EM35x Platform

If you are having the issue mentioned in the title after an update to EmberZnet 6.5.0.0 please consider updating to the Gecko Bootloader. If it is not an option for you the following is an explanation on why this problem occurs followed by a proposed solution. 

Although support of Ember Standalone Bootloader for EFR32 based products has ended in 2017. There could still be some devices in the field that were initially manufactured with the Ember Standalone Bootloader and are now unable to upgrade to the Gecko Bootloader. 

Since the 2.5 GSDK release modules are regarded as first class citizens and while the Gecko bootloader has been upgraded to facilitate this update the Ember Bootloader was not because it is no longer being developed. 

This update causes the AAT header in .ebl files built during the post-build process in Simplicity Studio to be interpreted as corrupt by the Ember Standalone Bootloader.

The problem is that the value of byte 0x78 used to be 0x10 for EFR32MG1P or 0x11 EFR32MG1B and after the update it is set to 0x01 for MGM111. 

If this is the issue the advised solution is to convert the created .s37 file to .ebl using the 'em3xx_convert' tool.
This should be located at "(StudioFolder)\developer\adapter_packs\em3xx\utils"

Open any command line tool at this location and you can convert a .s37 to .ebl with the correct AAT header using the following command. 

 "em3xx_convert.exe --chip EFR32 (path)/(filename).s37 (path)/(filename).ebl"