On CDT - Configuration Deployment Tool

Answer

Question: During CDT, some records were deleted from the Target database, why?
CDT was removing the records from the Target database because you might not have ignored the tables. That is, if there are additional records in the Target database that were not also present in the Source, they will be deleted.

Question: Some records were manually inserted in the Target database, but they are exactly the same as the Source database, except the keys (usually time stamp during creation). CDT is removing records from production, even though an equal record exists in source environment, why?
For the records to be treated as the same, all columns should have identical data.  If not, new records will be inserted.
  
Question: While promoting a certain table using CDT, some other table is manually ignored, but CDT also ignores other tables automatically, why?

During CDT, when a table is ignored while comparing/promoting, all the dependent tables are ignored as well.

Question: Is there any way to do the CDT based more on the business process, such as comparing certain records to see if they are the same, and deciding to promote based on the some other criteria?
Currently there is no such functionality which checks all records individually. However, to prevent existing data getting deleted from the Target database, promote the tables in “Append-only” mode (Refer to the corresponding documentation for more details). Once this is done, the target would have all the data, retaining its old one and updating only the new ones. All unwanted records can be manually deleted later.