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Make (one account) consistent with another, especially by allowing for transactions begun but not yet completed.
Since this sentence is using "reduce clause" and "allow for" is idiom, I suppose its meaning is as follows:
Make (one account) consistent with another, especially by allowing for transactions [that have] begun but [that are] not yet completed.
Taken from "Oxford Advanced Learner's Dictionary"
The second phrase in bold is not a sentence. A correct sentence would be, "One account was made to be consistent with another, especially by allowing for transactions to be begun but not yet completed."
The two are equivalent in every way except for the tense, which is different.
