The rx_freqlocked signal goes low in Lock to refclk (LTR) mode and goes high in Lock to Data (LTD) mode.

In addition, the CDR has
・ Auto-lock mode: CDR automatically transitions the loop from LTR to LTD
・Manual mode: User controls LTR and LTD loop using rx_locktorefclk and rx_locktodata
There are two modes of

In manual mode rx_freqlocked is ignored, but in autolock mode
rx_freqlocked is Low => High
You can judge that CDR has transitioned from LTR to LTD loop by .

Since Altera recommends auto-lock mode, rx_freqlocked is monitored in various reset sequences, so rx_freqlocked is basically a signal that should be monitored.

The transition timing from LTR to LTD is P27 of the ULR link below.
・ Figure 1-2. Lock Time Parameters for Manual Mode
・ Figure 1-3. Lock Time Parameters for Automatic Mode
Please refer to

 https://www.altera.com/en_US/pdfs/literature/hb/stratix-iv/stx4_siv54001.pdf