Question:
I want to be sure of something, is the use of k-fold cross-validation with time series is straightforward, or does one need to pay special attention before using it? 

Background:
I'm modeling a time series of 6 year (with semi-markov chain), with a data sample every 5 min. To compare several models, I'm using a 6-fold cross-validation by separating the data in 6 year, so my training sets (to calculate the parameters) have a length of 5 years, and the test sets have a length of 1 year. I'm not taking into account the time order, so my different sets are :


fold 1 : training [1 2 3 4 5], test [6]
fold 2 : training [1 2 3 4 6], test [5]
fold 3 : training [1 2 3 5 6], test [4]
fold 4 : training [1 2 4 5 6], test [3]
fold 5 : training [1 3 4 5 6], test [2]
fold 6 : training [2 3 4 5 6], test [1].


I'm making the hypothesis that each year are independent from each other. How can I verify that?
Is there any reference showing the applicability of k-fold cross-validation with time series.

Time-series (or other intrinsically ordered data) can be problematic for cross-validation.  If some pattern emerges in year 3 and stays for years 4-6, then your model can pick up on it, even though it wasn't part of years 1 & 2.

An approach that's sometimes more principled for time series is forward chaining, where your procedure would be something like this:


fold 1 : training [1], test [2]
fold 2 : training [1 2], test [3]
fold 3 : training [1 2 3], test [4]
fold 4 : training [1 2 3 4], test [5]
fold 5 : training [1 2 3 4 5], test [6]


That more accurately models the situation you'll see at prediction time, where you'll model on past data and predict on forward-looking data.  It also will give you a sense of the dependence of your modeling on data size.
