Interesting questions. Let's see if we can all figure this out together.
1) Is there any penalty for not complying to the EN harmonized standard?
Not specifically, but if you cannot otherwise prove to your Notified Body that you meet the Essential Requirements (ERs) of the applicable Directive, your right to apply the CE marking could be taken away. It is required to meet the applicable Essential Requirements (ERs) of the applicable European directive. Compliance with the harmonised standards, while not required, provides ‘presumption of conformity’ with the corresponding ERs. The alternative is somehow prove to the Notified Body that you meet the ERs in your own special way.
Here is some related info extracted from an EU guidance document on the New Approach Directives attached to a previous thread:
"The application of harmonised standards that give a presumption of conformity remains voluntary.The manufacturer can choose whether or not to refer to harmonised standards. However, if the manufacturer chooses not to follow a harmonised standard, he has the obligation to prove that his products are in conformity with essential requirements by the use of other means of his own choice (for example by means of any existing technical specifications). If the manufacturer applies only a part of a harmonised standard or the applicable harmonised standard does not cover all the essential requirements, the presumption of conformity exists only to the extent the standard corresponds to the essential requirements."
2) What is the penalty for quoting a standard in our technical file ER checklist which my company did not comply to?
I would not advise you to claim conformance to a standard that you do not conform with. There is a reasonable chance that your Notified Body (NB) would view this as a nonconformity. Perhaps you partially conform and can explain what aspects of the standard you do and do not conform with.
3) If my company really cannot comply with the new standards, can we just quoted the withdraw version instead?
I would prefer this over falsely claiming conformance to the current standard. This has to do with the "state of the art" and could be is tricky.
Since all standards are voluntary, there should be nothing wrong with claiming conformance to the older version of a standard. However, you might run into a concern from your NB that you are not in compliance with the first paragraph of MDD ER2 which states:
"The solutions adopted by the manufacturer for the design and construction of the devices must conform to safety principles, taking account of the generally acknowledged state of the art."
I wonder how NB's are going to deal with this.
4) Last of all what is the differences between EN ISO and ISO?
In my experience, the EN ISO version is typically identical to the corresponding ISO version except the year of the EN ISO version may be later, and the EN ISO version has an INFORMATIVE annex (not NORMATIVE annex) called something like this: "Relationship between the European Standard and the Essential Requirements of EU Directive 93/42/EEC". There is a table in this informative annex that cross-references the clauses of the standard to the ERs of the Directive. These cross-references are overly abundant in my opinion but they could be helpful for preparing an ER Checklist.
Here is an example of a standard where the EN ISO version only differs from the ISO version as I have indicated above.
EN ISO 11607-1:2009 Packaging for terminally sterilized medical devices - Part 1: Requirements for materials, sterile barrier systems and packaging systems (ISO 11607-1:2006)