A few issues to note and address up front ...
1/ Backup your data just before making any changes. Best to be safe hey!
2/ Your current list of completed and disqualified surveys are safe. No issues with them at all.
3/ If you make the changes, new surveys that have not started yet will see the new survey version (with the randomised blocks implemented). These will be fine also.
4/ The concerns surround the suspended / incompleted surveys. I would take a snapshot of the incompletes within the admin module just before you make the survey changes. You also have a backup of the data too. Consider the incompleted surveys that are suspended around the questions you are applying block randomisation to. These are the likely surveys that may encounter some missing data. Take a note of their sys_RespNum and monitor their activity / data through to the end of field work. Incompleted surveys that have not reached the block randomisation questions, or have passed them, will not encounter any issues.
5/ To summarise, I would make the changes at a quite surveying period. Around this time, backup your data, take a snapshot of the incompletes and note any sys_RespNum that hover around the block randomisation questions.
6/ Your new survey version data will have system generated data associated to the block randomisation that the version 1 survey will not have.
Does that all make sense? Let me know if you seek further clarification on any of the above.
Regards Paul. Stay safe and well.