Can I use AWS glue bookmarks to modify existing records

Since you talk about modifying existing ones, I'm going to assume you are talking about JDBC bookmarks and not s3 (in s3 you cannot update rows without updating files).
You can as long as you meet the requirement of having a numeric column monotonically increasing (for instance using a column with the update timestamp/version), so the bookmark can keep track of which rows to read, and in the case of updates you have your own logic to do an upsert (for instance using a temporary table and then doing a DB upsert into the final table).