I have noticed following bug when synchronizing scripts directory with database as source.
1) Create empty database
2) Create table.
3) Add partitioning info to the table.
4) Use SQL Compare to synchronize database to some empty folder with
option "Ignore filegroups, partitions schemes and partition functions" NOT checked.
Now we have table DDL with partitioning information added.
6) Drop partitioning from the table.
7) Synchronize database to scripts directory but now with "Ignore filegroups etc" checked.
8 ) Check DDL file for the table. Partitioning information is missing. It was overwritten. It should not be overwritten as option "Ignore filegroups, partitions schemes ..." was checked.
IMHO the behaviour in this case should be identical to database2database synchronization, when only ALTER's are generated by the tool, information which is set to be ignored on the options screen is really ignored not overwritten.
Issue exists in SQL Compare 9.0 (the latest version) and also in version 9.5 EA.