Unfortunately I don't think we can ever find out what actually happened. The earliest source, Gregory of Tours' Ten Books of History (c. 590), only says this:

But the third, Clodoald, they were unable to seize, since he was freed by the aid of brave men. He gave up his earthly kingdom and passed to the Lord's service, and cutting his hair with his own hand he became a clerk, busied with good works, and as a priest passed from this life.

The next earliest source, Pseudo-Fredegar's Chronicle (c. 660), provides a slightly different narrative, but it was even more brief:

Clodoald was forced into the clergy and led a worthy life.

So Gregory tells us that Clodoald was saved by others and joined the clergy seemingly out of his own accord (though we should not rule out pressure from others), whilst Pseudo-Fredegar outright says that Clodoald was forced to do so. Without further evidence, it is impossible to determine which narrative is more 'correct', or indeed if both authors painted a misleading picture of Clodoald's escape. We can perhaps speculate that simply by cutting off his hair, Clodoald was no longer in danger, as his brothers were apparently murdered because their grandmother refused to cut their hair (and thus lose their royal claims). However, there must have been quite a bit of personal and political manoeuvrings involved in their uncles' seizure of the young princes' lands, details that have now simply been lost to history, so ultimately we just don't have enough jigsaw pieces to piece together the puzzle of Clodoald's survival.

I should also add that there is a ninth-century hagiographical Life of Clodoald, but it was written to promote the sanctity of the Merovingian prince and its 'historical' content is essentially copied from Gregory of Tours. Even if it did contain more details, we would have analyse it very carefully, as its narrative would have been reshaped for three centuries by then and is therefore more of an indication of how later generations viewed the prince-turned-saint, rather than what actually happened in the sixth century.