Are you referring to the levels of muscle tone? By trying to induce permanent deformation to the tissues isn’t there a danger of compromising muscle stiffness?
Yes.
The change is not permanent. This is why EQIs have to be part of the program. They can’t simply be used once since intense work will cause the muscles to become contracted again (increase in tone).
That said, there are likely long-term beneficial adaptations that take place with EQIs, mainly at the tendon.
Is lowered muscle tone always necessary? Efficiency is dependent on optimal muscle tone. This will need to be assessed manually.
I believe when you stretch you should feel the stretch in the belly of the muscle not at the end ROM (at either end). For example, when doing a hamstring stretch you will want to feel the stretch in the middle of your leg and not towards your glutes or when doing a quad stretch you do not want to feel the stretch into your knees (i.e. remember those stretches where you put your shins on the ground and lean back till your back touches the ground). In conclusion, the stretch should be felt in the muscle and not at or near the tendons!
Note: the above refers to static stretching.
BTW, just so everybody’s on the same topic EQI’s refer to Extended Quasi Isometrics, correct?
P.S. I like to stretch before sprinting but not before lifting. When a limb moves through a greater range of motion at a higher velocity it has the biggest potential for injury. That is why I like doing static and dynamic stretching before spriting. Also, if you think about it, in powerlifting when you do your warmup sets you are in effect dynamically stretching; so therefore, you don’t have to statically stretch. I have never received an injury by not statically stretching before a lifting session; although, I did obtain injuries when my core temperature was not high enough (i.e. I skipped the 10 mins of riding the bike so to speak).
Eccentric Quasi Isometrics
I knew I was close. 
Thanks for the clear up. My best friend’s boxing coach does these along with other westside stuff and he coach now bench’s 600lbs. Whether or not he uses a WL bench suit is another question I should ask him that next time we speak.
Just wanted to get people’s opinion on this,
http://www.charliefrancis.com/community/showpost.php?p=87015&postcount=78
You can post your reply at the above thread topic so as not to derail this one.
Thank you.
Tony, you wrote that EQI’s work “By re-lengthening the muscle (structural change) you restore flexibility while increasing the ability of the muscle to produce force, recover, etc. This is what EQIs do.”
Sorry but I need it broken down to simpelton terms cause I am an idiot:
EQI’s 1) Promote recovery due to the muscle being worked for a certain time period where more blood flow will rush to the area causing more nutrient/gas echange at the area being worked than if you were just resting it. Am I way off?
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You restore flexibility in the muscle, I would assume cause it is stretching
, but by having the muscles still producing force while in this stretched postion you are teaching the muscles to strengthen at more disadvantages positions which should lead to a carryover in strength at other joint angles? Am I off on this too? 
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In CT"s book, you wrote that EQI’s “are simply an eccentric action.” The main difference in terms of of typical eccentric used just to lower the weight and these are that the EQI’s work the muscles in a stretched and often weak position. By working in this weak position one can shift the length-tension curve. Am I correct in these assumptions or way off???
I will ask more later on these but let me know if I am understanding these concept correctly or if like much of my life are just passing me by!
Thanks for any info
PEACE
Lowered muscle tone is not always necessary or desirable. As you stated, muscle tone needs to be at an optimal level, which can be determined manually.
I can tell you have read the chapter.
The increase in bloodflow has some implications for recovery for certain, but this is not where I believe most of the recovery benefits of EQIs come from.
As I stated above, EQIs can relengthen the muscle. If the muscle is left in a contracted state it will not be able to recover. This is where I believe most of the recovery benefits of EQIs are.
You are correct that an isometric contraction in the stretched position will lead to a better transfer of strength gains at all joint angles. However, the load for EQIs should be relatively light (at least initially), so I would recommend isometric holds in the stretched position with a higher load for a shorter duration in order to derive the benefits you are referring to.
Yes, EQIs are simply an eccentric action. However, the speed at which an eccentric action is performed has great implications for the benefits you will derive (ex. altitude landings vs. EQIs). It is certainly possible that by training for long periods of time in the stretched position that the length-tension curve can be shifted.
Tony, have you used the Therastim with the EQIs and if so what are your thoughts?
The Therastim and EQIs serve similar functions so I do not combine the two.