How to understand "homomorphically decrypting" in bootstrapping?
Does it mean decrypt to the plaintext first then recrypt again?


No. It doesn't. It just mean to run a "homomorphic version" of the decryption function. Since homomorphic evaluation just use homomorphic operations and these operations always return ciphertexts, the result of homomorphic decryption is also a ciphertext. And since the decryption removes the noise, this new ciphertext is fresh.

Think of evaluating homomorphically as a function, which we will call $Eval$. 

So, homomorphically evaluating any function $f$ on arguments $m_0$, $m_1$, ..., $m_\ell$ means to execute $Eval(pk, f, [m_0]_{pk}, [m_1]_{pk}, ..., [m_\ell]_{pk})$, which returns $[f(m_0, m_1, ..., m_\ell)]_{pk}$.

(Here I'm using $[m]_{pk}$ to denote the encryption of $m$ under the public key $pk$).

That is, $Eval$ returns an encryption of the function evaluated in the arguments, given the function, encryptions of those arguments, and the public key used to encrypt them.

Now, let's say you have a pair of keys $sk$ and $pk$ and you want to refresh a ciphertext $c = [m]_{pk}$. Then, you have to homomorphically decrypt $c$. To do so, replace $f$ by $Dec$. Also, the arguments of $Dec$ are $sk$ and $c$, so, you should use $[sk]_{pk_1}$ and $[c]_{pk_1}$, for some public key $pk_1$. Then, we get:

$\begin{align}
Eval(pk_1, Dec, [sk]_{pk_1}, [c]_{pk_1}) &amp;= [Dec(sk, c)]_{pk_1}\\
                                       &amp;= [m]_{pk_1}\\
\end{align}$

that is, a fresh encryption of $m$ under the public key $pk_1$.

Note that this $pk_1$ may be a new public key, and in this case we will need a new secret key $sk_1$ to decrypt $[m]_{pk_1}$, or it can be equal to the original public key $pk$, and in this case we are supposing circular security...