Given a sequence of natural numbers $f:\mathbb{N}\to\mathbb{N}$ define a new sequence $\phi f$ as follows:
$$ \phi f(n):=|\{ k\in\mathbb{N} \mid k \leq n,f(k)=f(n)\}|$$
In other words $\phi f(n)$ counts up how often $f(n)=f(k)$ for $k\leq n$. Also, we can apply $\phi$ iteratively, e.g.:
$$\begin{array}{rcl} \\ f & = & (0,&1,&0,&2,&1,&3,&0,&2,&0,&1,&...) \\ \phi f & = & (1,&1,&2,&1,&2,&1,&3,&2,&4,&3,&...) \\ \phi^2 f & = & (1,&2,&1,&3,&2,&4,&1,&3,&1,&2,&...) \\ \phi^3 f & = & (1,&1,&2,&1,&2,&1,&3,&2,&4,&3,&...) \\ & \vdots \end{array}$$
Notice that $\phi f=\phi^3 f$. My conjecture is thus for any sequence of natural numbers $f$, we have $\phi^{n+1} f = \phi^{n+3} f$ for all $n\in\mathbb{N}$.
Very nice observation.
As you note, for the conjecture it suffices to prove $\phi^3=\phi$.
Call sequences $a=(a_1,a_2,\dots)$ and $b=(b_1,b_2,\dots)$ similar, if $\phi a=\phi b$, i.e. for each index $n$, $\ a_n$ occurs the same times among $a_1,\dots,a_n\ $ as $\ b_n$ among $b_1,\dots,b_n$.
For example, the sequences $(1,1,2,2,3,3,1),\ (1,1,2,2,3,3,2),\ (1,1,2,2,3,3,3)$ are similar.
We have to show that $\phi^2 a$ is similar to $a$ for an arbitrary sequence $a$.
Assume it holds for $n$ long sequences, and take $a_{n+1}$ in $a=(a_1,\dots,a_{n+1})$.
This $s$ occurs in $\phi a$ for exactly $q$ times, where $q$ is the number of $a_i$'s occuring exactly $s$ times in $a$. (If $s$ is new, then $q=1$, and $a_{n+1}$ can be replaced by any of these $a_i$'s to get a similar sequence.)
On one hand, it means $\phi^2 a(n+1)=q$.
On the other hand, $q$ already occured in $\phi^2 a(1,\dots,n)$ exactly $s-1=|\{i\le n:a_i=a_{n+1}\}|$ times.
Another approach
Call a sequence $a$ of positive integers a regular sequence, if for all $n$,
Note that 2. can be rephrased as: if $a_n=a_i$ for some $i<n$, then $a_n$ is minimal among those sequence elements which occur exactly $(\phi a)_n-1$ times in $(a_1,\dots,a_{n-1})$
[because $a_n$ in $(a_1,\dots,a_n)$ has one more occurances than any of them].
For example, $(1,2,2)$ and $(1,2,3,2)$ are not regular, while $(1,2,1)$ and $(1,2,3,1)$ are regular.
Proposition.
$\ $ a) $\ \phi a$ is regular for any sequence $a$.
$\ $ b) $\ $If $a$ is a regular sequence, then $\phi^2 a=a$.