Question on timing in 48-hr subs in PvE

Yepyep said:

So I could use some advice. In a 48-hr sub, typically one does 4 clears of each node, then clear #5 at 0+24 hrs, then #6 at 0+48 hrs.

My question is this: if I don't do the first 4 clears until say, hour 0+12, when should I do clear #5? At hour 0+24 or at hour 0+36? 

A related question: what is the best timing for the orange starter node, the one with required characters, in a 48-hr sub? Clear #1, then #2 at 0+24, then #3 at 0+48? Maybe the timing doesn't matter...?

Hopefully my question is clear, it's kind of hard to state clearly. Thanks very much! 

For 48-hr subs, you always want to do all initial clears until you see the timer with reduced points, so that'll be 4x for regular nodes, 2x for wave nodes, and 1x for the loaner node (the orange starter node you mentioned). Then, do your one clear (#5 for regular node, #3 for waves, #2 for loaner) 24 hours after your initial clears when the points have refreshed in full (and the timer is gone). Finally, do the remaining 3 clears (#6-8 for regular node, #4-6 for waves, #3-5 for loaner) as close to the end of the sub as possible. 

So if you do your first 4 clears at hour 0+12, then clear #5 will be at hour 0+36 (when the timer is gone and the points are back at their full amount)

The orange starter node should be clear #1 at hour 0, clear #2 at 0+24, and clears #3-5 at right before hour 0+48.

ETA: As stated below, it doesn't matter if the timer is still there as long as the points have fully refreshed. But if you can't remember what the full point amount is, you can wait for the timer to go away to be safe, or you can check this spreadsheet: http://tinyurl.com/MPQ-PVE-Details 

If the refresh counter is still there, reading 5 mins 20 s for example, but the points have fully recharged. Does it matter if you Replay the node before the refresh counter is gone at 4 mins 19 s? Will it affect the points accumulated for the 6,7,8 hits?