On 23 August 2007, the Human Rights Committee released a new General Comment on article 14 (Right to equality before courts and tribunals and to a fair trial) of the International Covenant on Civil and Political Rights (ICCPR). While this General Comment goes into great detail about almost every aspect of a trial - which is of no interest here - it also deals with the issue of repeated imprisonment of conscientious objectors.
The relevant paragraphs are:
IX. Ne bis in idem
54. Article 14, paragraph 7 of the Covenant, providing that no one shall be liable to be tried or punished again for an offence of which they have already been finally convicted or acquitted in accordance with the law and penal procedure of each country, embodies the principle of ne bis in idem. This provision prohibits bringing a person, once convicted or acquitted of a certain offence, either before the same court again or before another tribunal again for the same offence; thus, for instance, someone acquitted by a civilian court cannot be tried again for the same offence by a military or special tribunal. Article 14, paragraph 7 does not prohibit retrial of a person convicted in absentia who requests it, but applies to the second conviction.
55. Repeated punishment of conscientious objectors for not having obeyed a renewed order to serve in the military may amount to punishment for the same crime if such subsequent refusal is based on the same constant resolve grounded in reasons of conscience.
Sources: General Comment No. 32, CCPR/C/GC/32, 23 August 2007