In 1598 Elizabeth I passed a law requiring that a copy of each church’s parish register should be sent to the bishop who had jurisdiction over the parish, within one month of Easter every year. These are the bishop’s transcripts (sometimes also called Archdeacon Transcripts).
They make a useful backup to parish registers and should be checked if you cannot find one of these, as they often fill in gaps where a register has gone missing. In general however, the transcripts are usually less complete than the originals. As with parish registers none at all survive from the Commonwealth period between 1649 and 1660.
At the time they would have been kept in the diocesan registry, but nowadays nearly all of them can be found in your county record office. Some universities and the occasional church library do still have copies. You should be aware that as they were copied contemporarily by hand, some will contain errors, omissions or even additions compared to the original. Also, until 1752, years run from the 25th of March to the 24th March.