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A great number of the men who signed off on the 1st London Confession also signed off on the 2nd London Confession (cf. Dr. James Renihan, The Baptist Confession of Faith, Foreword). According to Nehemiah Coxe and William Collins in their ‘Letter to the Judicious and Impartial Reader’ prefacing the 2nd London Confession, it was the year 1643 when the 1st London Confession appeared on the scene (it was probably actually published in 1644).
Because of the limited scope of that first confession, note Coxe and Collins, the Baptist position was being misconstrued to the public. Baptists were being accused of holding beliefs they did not hold to. So, it seemed to good to the pastors of the Petty France Church in London to edit a 2nd, more comprehensive, confession. This confession would come to be called the 1689 London Baptist Confession of Faith.
Though the 1st London was initially signed by representatives of only seven congregations, its theology came to be widely recognized by many Baptist churches in England and Wales. Moreover, many of the signees of that document went on to endorse the newly edited 2nd London Confession.
In order to preserve orthodoxy and demonstrate unity, the 2nd London Confession built off the backs of the Westminster Confession, the Westminster Larger and Shorter Catechisms, and the Savoy Declaration and Platform of Polity. This explains the great overlap of language between the 2nd London Confession and these other documents. More agreement than difference is found among these confessions––agreement not particularly apparent in the 1st London Confession (because it was too narrow in scope).
Therefore, it is not as if the theology of the 1st London is at variance with the 2nd. Rather, the first has identical doctrinal substance as the second. Many of the same men were involved in drafting both, and there is no evidence those men changed their doctrinal positions in the time between the 1st and 2nd Confessions.
Digital copies of both the 1st London and the 2nd London Confessions can be found at the links below: