WRONG
In case when the Lessee does not acquire a building permit before 30 June 2014, the Lessor has the right to terminate the lease agreement upon one month’s notice.

RIGHT
If the Lessee does not acquire a building permit before 30 June 2014, the Lessor has the right to terminate the lease agreement upon one month’s notice.

The phrases “in case when” or “in the case when” do not exist in English. Instead, use “if”. You may use “in the event that”, but there is rarely any reason to do this, unless you think your client will be impressed by four words when one is enough. (Native English speakers will not.)

Also, don’t translate “gdy” as “when” in conditional sentences – use “if”:

WRONG
In accordance with § 9 Section 3, the Lessor has a right to terminate the Lease Agreement when the Lessee does not commence construction before 31 December 2016.

RIGHT
In accordance with § 9 Section 3, the Lessor has a right to terminate the Lease Agreement if the Lessee does not commence construction before 31 December 2016.

For more information see the entry How to use “in case”.