Here is a way :
$a = Get-Content 'D:\temp\mytest.json' -raw | ConvertFrom-Json
$a.update | % {if($_.name -eq 'test1'){$_.version=3.0}}
$a | ConvertTo-Json -depth 32| set-content 'D:\temp\mytestBis.json'
According to @FLGMwt and @mikemaccana I improve the ConvertTo-Json
with -depth 32
because the default depth value is 2 and for object deeper than 2 you will receive class informations in spite of objects.