It’s not advisable to modify the besclient.config via script. The best practice is to update BES settings via BigFix action/content? Please review the client settings fixlets available from @jgstew.
Are you setting AdvertismentList and SeekList on the BESRelays and BESClients respectively?
Really need to know if your network is blocking ICMP at any point on your LAN.
Please see the platform documentation on relay affiliation and @JasonWalker forum post on relay SeekList process.