GA C5.4.7 5.4.7.

Does the filing of amendments have an impact on the number of claims fees payable? 
5.4.032
The claims fees are calculated on the basis of the number of claims contained in the application in the version that is, in accordance with the indications in Form 1200, to be taken as the basis for the procedure in the European phase. The amount of the claims fee varies according to a two-tier system. For the 16th and each further claim a claims fee must be paid. However, for any claim over 50 a higher amount is due (see points 5.11.004 ff).
5.4.033
Where claims fees are to be paid, they must be paid within the 31-month time limit. If the applicant fails to pay (the correct amount of) claims fees in due time, he is invited in the Rule 161/162 communication to pay the missing amount within the non-extendable six-month time limit set therein (see point 5.4.013). If the number of claims increases due to (further) amendments filed in reply to the Rule 161/162 communication, any claims fees due for the additional claims must also be paid within the six-month time limit (see point 5.11.009). If a supplementary European search is carried out, it will relate to the last set of claims received before expiry of the six-month time limit and will be confined to claims for which any claims fees, where applicable, have been paid in due time.
5.4.034
Where the number of claims changes as a consequence of a (further) amendment submitted within the six-month time limit set in the Rule 161/162 communication (see point 5.4.013), that number is decisive for calculating the amount of the claims fees to be paid.
5.4.035
If consequent to the amendments made before expiry of the six-month time limit the number of claims forming the basis for the further procedure is reduced, any claims fees overpaid will be refunded. 
5.4.036
Claims for which a fee due is not paid are deemed to be abandoned, and the applicant is notified thereof. The loss of rights may be remedied by further processing. Features of a claim deemed abandoned which are not otherwise to be found in the description cannot be reintroduced into the application. 

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EPC Articles

EPC Implementing Rules

EPC Rules relating to Fees

EPO Guidelines - E General Procedural Matters

EPO Guide for Applicants, part II Int.

EPO Guide for Applicants, part II Int. - C The EPO as ISA and SISA

Offical Journal of the EPO

General Case Law