The problem is not specific to Sqlite3DS (TSqlite3Dataset). Any package that depends of fpc native sqlite3 unit will have the same problem.
This occurs because the compiler find fpc sqlite3 unit and then find sqlite3 wrapper unit. Since the checksum of the two units does not match, the compiler tries to recompile Sqlite3DS.
Most of the time removing the package unit (sqlite3laz) from uses clause of main project file, resolves the issue.