There are several methods to approach the situation and it depends on whether there's a currently running dirsync in the project.
Ideally, source domain objects' stamping should be cleaned either manually or using PowerShell scripts.
If there's no dirsync configured and running for the current domain pair, then it's possible to change stamping attributes for the source domain in domain pair properties, Object Matching, Service Attributes, select drop-down for the source domain and class. Then select 2 currently unused attributes.
If dirsync is configured and running, the only alternative way to address the issue is to setup a separate QMM project/ADLDS database, with its own DSA and configure a completely different set of stamping attributes for source and target domains, then migrate affected accounts.