Captain Thomas Boulds or Bowles of Dublin

Most of the references we have for these Bowles are not from images of the original paper, just from transcriptions of those early documents.  Most of these were made in the late 1800's. In that later period Bowles had become the most common spelling of the name.  Many or even most transcribers may have been trying to be helpful by transcribing an entry like Boules as Bowles. Granted the 1600's script can be very difficult now for many of us to read without a lot of practice and they were often right that the name had evolved from Boules to Bowles but they may also have been making an incorrect assumption.  Back in the 1600's the spelling of surnames was pretty erratic, mostly because it generally just didn't matter.  A clerk recording a church event would write down whatever the family name(s) sounded like to him.  Often that would be based on local spellings of a similar sounding name he was already familiar with.  See Origin of the Bowles Name  Bolle/Bolles and Bold/Bould are two of the phonetically-spelled common early names of families that later became Bowles.

Now a very important point: not a single one of the contemporary (original) references I have found for this family have used the Bowles spelling until 1683 when the first 'w' appears in the name in the registry entry for Hester Bowles marriage to William Stowell.  After that the next 'Bowles' spellings that I could find in original scripts were in Deed Memorials starting in 1715. 

The Whitshed family recorded Thomas Sr. as Captain Boules who married Mary Plunket (see the Whitshed/Plunket reference below) and his burial record lists him as Captain Thomas Bolds. 
The baptism of Thomas and Mary's first child at St Johns Dublin was recorded as to Thomas Bold but the next three baptized there were to Thomas Bould and their next, baptised at St Brides Dublin, was to parents Thomas and Mary Boale.  Their son Thomas Jr's burial was recorded as Mr Boulds.  Thomas Jr's son Charles baptismal entry was spelled Bould. 

Their daughter Hester was baptized as Bould in 1655 but her marriage in 1683 records her as Bowles.  After that I couldn't find the Bowles spelling in an original document until the Deed Memorials involving his grandchildren starting in 1715.

Based on all these early original source references it would appear that it was a Captain Thomas Bould/Bold/Bolds who came from England in 1649/50 and that we should search in those lines for his origin in England.  Perhaps the 19th century transcribers were wrong to convert his name to Bowles in their records.  I don't believe so.  The 'w' had appeared in most of the prominent Bowles families in England by the mid-1600's.  However, Bowles was virtually unknown in Dublin.  One branch of the prominent Thomas Boles of Cork line adopted that spelling only in the 1760's with George Bowles of Mount Prospect, co. Cork (son of Robert Boles of Springfield, co. Cork).  In the also prominent Richard Boles of Cork line the first 'w' that I can find is a reference in the Friends Book of Sufferings for Abigail Bowles in 1698, although her family typically used the Boles spelling, and the next would be the request made by John Boles (then of Ballintrane, co. Carlow) request to be given permission to marry Susan Nicholson in 1701 which is recorded in the Carlow Meeting Minutes which in one sentence uses both 'John Bowles' and 'John Boles'.  I can't find any original source references for a Bowles spelling actually in Dublin that early.