Hello Divya. If this happens during a Refresh Identity Cube task with only Refresh identity attributes enabled, it matches a defect SailPoint fixed in IdentityIQ 8.5 under IIQTC-626. The defect caused an identity attribute value to be removed when the identity no longer had an account for the associated application source-mapping rule.
Could you confirm your IIQ version, patch level, and the options enabled on the refresh task?
If you are on 8.5 or later and the same scenario still reproduces, I would open a SailPoint Support case and reference IIQTC-626. If you are below 8.5, upgrading would be the cleanest fix, or you could check with Support whether the fix is available for your current version.