Custom .idb file changes in the $SPECROOT/lib/SDPM directory are overwritten during a Spectrum Upgrade.
This is functioning as designed. You can backup the modified .idb files using the preUpgradeBackup.sh script referenced in the following knowledge document.
https://knowledge.broadcom.com/external/article?articleNumber=239419
An enhancement request has been submitted to preserve the modified .idb files during an upgrade.